Genome Analysis Wiki - User contributions [en]

Regions of high linkage disequilibrium (LD)

2021-10-11T02:38:39Z

Mflick:

There are regions of long-range, high linkage diequilibrium in the human genome <ref>Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147</ref><ref>Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

[[Image:High-ld-b38.png]]

Here is a list of positions for GRCH Build 38. There positions are provided by the [https://github.com/cran/plinkQC/blob/master/inst/extdata/high-LD-regions-hg38-GRCh38.bed plinkQC R package] and were provided by Anderson2010<ref>Anderson, Carl A., et al. "Data quality control in genetic case-control association studies." Nature protocols 5.9 (2010): 1564-1573.</ref>
<tab border="1" head="top">
Chr Start Stop
chr1 47761740 51761740
chr1 125169943 125170022
chr1 144106678 144106709
chr1 181955019 181955047
chr2 85919365 100517106
chr2 87416141 87416186
chr2 87417804 87417863
chr2 87418924 87418981
chr2 89917298 89917322
chr2 135275091 135275210
chr2 182427027 189427029
chr2 207609786 207609808
chr3 47483505 49987563
chr3 83368158 86868160
chr5 44464140 51168409
chr5 129636407 132636409
chr6 25391792 33424245
chr6 26726947 26726981
chr6 57788603 58453888
chr6 61109122 61357029
chr6 61424410 61424451
chr6 139637169 142137170
chr7 54964812 66897578
chr7 62182500 62277073
chr8 8105067 12105082
chr8 43025699 48924888
chr8 47303500 47317337
chr8 110918594 113918595
chr9 40365644 40365693
chr9 64198500 64200392
chr9 88958735 88959017
chr10 36671065 43184546
chr10 41693521 41885273
chr11 88127183 91127184
chr12 32955798 41319931
chr12 34639034 34639084
chr14 87391719 87391996
chr14 94658026 94658080
chr17 43159541 43159574
chr20 4031884 4032441
chr20 33948532 36438183
chr22 30060084 30060162
chr22 42980497 42980522
</tab>

Here is a list of positions for GRCH Build 37

[[Image:High-ld.png]]

<tab border="1" head="top">
Chr Start Stop
1 48000000 52000000
2 86000000 100500000
2 134500000 138000000
2 183000000 190000000
3 47500000 50000000
3 83500000 87000000
3 89000000 97500000
5 44500000 50500000
5 98000000 100500000
5 129000000 132000000
5 135500000 138500000
6 25000000 35000000
6 57000000 64000000
6 140000000 142500000
7 55000000 66000000
8 7000000 13000000
8 43000000 50000000
8 112000000 115000000
10 37000000 43000000
11 46000000 57000000
11 87500000 90500000
12 33000000 40000000
12 109500000 112000000
20 32000000 34500000
</tab>

These positions are for GRCH build 36.
<tab border="1" head="top">
Chr Start Stop ID
1 48060567 52060567 hild1
2 85941853 100407914 hild2
2 134382738 137882738 hild3
2 182882739 189882739 hild4
3 47500000 50000000 hild5
3 83500000 87000000 hild6
3 89000000 97500000 hild7
5 44500000 50500000 hild8
5 98000000 100500000 hild9
5 129000000 132000000 hild10
5 135500000 138500000 hild11
6 25500000 33500000 hild12
6 57000000 64000000 hild13
6 140000000 142500000 hild14
7 55193285 66193285 hild15
8 8000000 12000000 hild16
8 43000000 50000000 hild17
8 112000000 115000000 hild18
10 37000000 43000000 hild19
11 46000000 57000000 hild20
11 87500000 90500000 hild21
12 33000000 40000000 hild22
12 109521663 112021663 hild23
20 32000000 34500000 hild24
X 14150264 16650264 hild25
X 25650264 28650264 hild26
X 33150264 35650264 hild27
X 55133704 60500000 hild28
X 65133704 67633704 hild29
X 71633704 77580511 hild30
X 80080511 86080511 hild31
X 100580511 103080511 hild32
X 125602146 128102146 hild33
X 129102146 131602146 hild34
</tab>

== Excluding Regions With Plink ==

You can remove these regions from a PED file using the following PLINK commands. Assuming you have the data stored in a file named "high-ld.txt"

plink --file mydata --make-set high-ld.txt --write-set --out hild
plink --file mydata --exclude hild.set --recode --out mydatatrimmed

= References =

<references />

File:High-ld-b38.png

2021-10-11T02:38:04Z

Mflick:

Regions of high linkage disequilibrium (LD)

2021-10-10T03:12:00Z

Mflick:

There are regions of long-range, high linkage diequilibrium in the human genome <ref>Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147</ref><ref>Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

[[Image:High-ld.png]]

Here is a list of positions for GRCH Build 38. There positions are provided by the [https://github.com/cran/plinkQC/blob/master/inst/extdata/high-LD-regions-hg38-GRCh38.bed plinkQC R package] and were provided by Anderson2010<ref>Anderson, Carl A., et al. "Data quality control in genetic case-control association studies." Nature protocols 5.9 (2010): 1564-1573.</ref>
<tab border="1" head="top">
Chr Start Stop
chr1 47761740 51761740
chr1 125169943 125170022
chr1 144106678 144106709
chr1 181955019 181955047
chr2 85919365 100517106
chr2 87416141 87416186
chr2 87417804 87417863
chr2 87418924 87418981
chr2 89917298 89917322
chr2 135275091 135275210
chr2 182427027 189427029
chr2 207609786 207609808
chr3 47483505 49987563
chr3 83368158 86868160
chr5 44464140 51168409
chr5 129636407 132636409
chr6 25391792 33424245
chr6 26726947 26726981
chr6 57788603 58453888
chr6 61109122 61357029
chr6 61424410 61424451
chr6 139637169 142137170
chr7 54964812 66897578
chr7 62182500 62277073
chr8 8105067 12105082
chr8 43025699 48924888
chr8 47303500 47317337
chr8 110918594 113918595
chr9 40365644 40365693
chr9 64198500 64200392
chr9 88958735 88959017
chr10 36671065 43184546
chr10 41693521 41885273
chr11 88127183 91127184
chr12 32955798 41319931
chr12 34639034 34639084
chr14 87391719 87391996
chr14 94658026 94658080
chr17 43159541 43159574
chr20 4031884 4032441
chr20 33948532 36438183
chr22 30060084 30060162
chr22 42980497 42980522
</tab>

Here is a list of positions for GRCH Build 37
<tab border="1" head="top">
Chr Start Stop
1 48000000 52000000
2 86000000 100500000
2 134500000 138000000
2 183000000 190000000
3 47500000 50000000
3 83500000 87000000
3 89000000 97500000
5 44500000 50500000
5 98000000 100500000
5 129000000 132000000
5 135500000 138500000
6 25000000 35000000
6 57000000 64000000
6 140000000 142500000
7 55000000 66000000
8 7000000 13000000
8 43000000 50000000
8 112000000 115000000
10 37000000 43000000
11 46000000 57000000
11 87500000 90500000
12 33000000 40000000
12 109500000 112000000
20 32000000 34500000
</tab>

These positions are for GRCH build 36.
<tab border="1" head="top">
Chr Start Stop ID
1 48060567 52060567 hild1
2 85941853 100407914 hild2
2 134382738 137882738 hild3
2 182882739 189882739 hild4
3 47500000 50000000 hild5
3 83500000 87000000 hild6
3 89000000 97500000 hild7
5 44500000 50500000 hild8
5 98000000 100500000 hild9
5 129000000 132000000 hild10
5 135500000 138500000 hild11
6 25500000 33500000 hild12
6 57000000 64000000 hild13
6 140000000 142500000 hild14
7 55193285 66193285 hild15
8 8000000 12000000 hild16
8 43000000 50000000 hild17
8 112000000 115000000 hild18
10 37000000 43000000 hild19
11 46000000 57000000 hild20
11 87500000 90500000 hild21
12 33000000 40000000 hild22
12 109521663 112021663 hild23
20 32000000 34500000 hild24
X 14150264 16650264 hild25
X 25650264 28650264 hild26
X 33150264 35650264 hild27
X 55133704 60500000 hild28
X 65133704 67633704 hild29
X 71633704 77580511 hild30
X 80080511 86080511 hild31
X 100580511 103080511 hild32
X 125602146 128102146 hild33
X 129102146 131602146 hild34
</tab>

== Excluding Regions With Plink ==

You can remove these regions from a PED file using the following PLINK commands. Assuming you have the data stored in a file named "high-ld.txt"

plink --file mydata --make-set high-ld.txt --write-set --out hild
plink --file mydata --exclude hild.set --recode --out mydatatrimmed

= References =

<references />

User talk:Alaa El Banna

2021-09-04T23:04:25Z

Mflick: Welcome!

'''Welcome to ''Genome Analysis Wiki''!'''
We hope you will contribute much and well.
You will probably want to read the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents help pages].
Again, welcome and have fun! [[User:Mflick|Mflick]] ([[User talk:Mflick|talk]]) 19:04, 4 September 2021 (EDT)

User:Alaa El Banna

2021-09-04T23:04:25Z

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I have a bachelor degree in medicine and general surgery and a masters degree in chemical pathology from Alexandria university , Egypt.
I am working on my PHD from the same department , my thesis topic is regarding miRNA expression in Autistic disorders to be used for assessment of severity and personalized medicine .
Besides that I am working on a project regarding genome sequencing in COVID cases for determination of susceptibility to severe forms of infection.

User talk:Workneh

2021-08-31T16:59:57Z

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User:Workneh

2021-08-31T16:59:56Z

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starting my carrier as a biologist and now I am focusing on molecular biology and molecular diagnostics and bioinformatics. Especially identification and development of molecular biomarkers in disease diagnostic, prognostic, and therapeutics. Especially, the search for molecular markers from transcriptomics is my prior area where our team is currently working.

User talk:Kaskere

2021-05-06T20:44:48Z

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User:Kaskere

2021-05-06T20:44:47Z

Mflick: Creating user page for new user.

I am molecular geneticist, currently doing PhD and working in bioinformatics field. For 5 years I was working with infertility genetics, and also doing further researches in particular field. I am passionate about programming and molecular biology. I learn how to run new biostatistics tools, with special interest in burden tests.

User talk:Ronypcolanzi

2020-11-15T00:34:21Z

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User:Ronypcolanzi

2020-11-15T00:34:20Z

Mflick: Creating user page for new user.

I was born on March 3, 1956. I am a pathologist. I have been working since 1987 at the Japanese hospital in Santa Cruz-Bolivia. I have been working since 1987 at the Catedral Laboratory in Santa Cruz-Bolivia. I have taken courses in gastrointestinal pathology in Japan. Forensic pathology course in the USA. Professor of Legal Medicine at the Private University of Santa Cruz. Professor of Pathology at the Catholic University of Santa Cruz. I have done masters in genetics. Currently doing a master's degree in thrombosis and genetics.

User talk:Cusackse2

2020-11-06T06:15:04Z

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User:Cusackse2

2020-11-06T06:15:03Z

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PhD candidate in Clinical Psychology who conducts research at the intersection of PTSD and alcohol use, with a focus on protective factors. I am receiving training in statistical genetics via my F31 training grant. I am currently conducting my dissertation study using GWAS, GCTA, and PRS to examine the genetic overlap between constructs relevant to traumatic stress.

User talk:Afshin

2020-09-21T22:18:46Z

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User talk:Ttbek

2020-06-02T15:03:05Z

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User:Ttbek

2020-06-02T15:03:04Z

Mflick: Creating user page for new user.

Khalid Kunji is a Umich (BS Biophysics and Pure Mathematics) and UM-Flint (MS Computer Science) alumni working on GWAS and other bioinformatics related projects at Qatar Computing Research Institute, a part of Hamad Bin Khalifa University and Qatar Foundation. His work focuses on the application of machine learning and statistics to predicting protein properties, doing imputation in family data, and whole genome GWAS.

User talk:Sunyidsjtu

2020-02-27T16:21:15Z

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User:Sunyidsjtu

2020-02-27T16:21:09Z

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My name is Yidan Sun and I am a graduate student at Shanghai Jiao Tong University. I expect to gain a master’s degree by June 2021. My current research is using Genome-Wide Association Studies (GWAS) to identify genetic markers associated with drug-induced liver injury (DILI) and doing Polygenic score analyses on DILI

User talk:Cindydongjing

2019-11-12T21:10:59Z

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User:Cindydongjing

2019-11-12T21:10:58Z

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I am a CPRIT-funded postdoc associate in integrative cancer epidemiology at Baylor College of Medicine. My research interests are to identify genetic variants that are associated with cancer susceptibility and prognosis. Using genome-wide association analysis, genome-wide gene-environment interaction analysis, and NGS approaches, I have identified dozens risk loci for cancers.

User talk:NikiMourtzi

2019-10-28T16:23:49Z

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User:NikiMourtzi

2019-10-28T16:23:49Z

Mflick: Creating user page for new user.

Ms. Mourtzi is currently a PhD student, National and Kapodistrian University of Athens, doing an intership within CHDM whose research in our laboratory focuses on synthesizing informatics tools in families with pediatric endocrine disorders to decipher the genetic architecture of these disorders. She will also participate in broader experimental lines of investigation pertaining to the genetic architecture of human pediatric disorders. Ms. Mourtzi's research interest revolve around endocrine and neurological diseases. She has participated in the HELIAD study with her research focusing on exploring the genetic/environmental factors associated with frailty syndrome. She has also investigated the role of lncRNAs in human breast milk exosomes from mothers with premature and mature birth.

User talk:Bongo

2019-10-02T17:43:58Z

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User:Bongo

2019-10-02T17:43:58Z

Mflick: Creating user page for new user.

My name is Bongo, I am in grad school complete a PhD degree in animal breeding and genetics. I am based in South Africa. My interest is in the genomics field, investigating underlying factors that affect certain fertility in cattle. I like making associations between genes and phenotypes especially in cattle

User talk:Hoosier060

2019-06-06T18:41:40Z

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User:Hoosier060

2019-06-06T18:41:39Z

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Bioinformatics Scientist at Leidos Biomedical Research, Inc./NCI/NIH
I do GWAS analysis/have been doing GWAS for past 10 years at NCI with investigators.
Many imputation work has been done with the Michigan Imputation Server which uses minimac3.
I would like to run in house minimac4 pipeline specifically for X

BAFRegress

2018-07-18T21:09:53Z

Mflick:

[[Category:Software|BafRegress]]

'''bafRegress''' is a software that detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model.

== Download bafRegress ==

* [[File:bafRegress.tar.gz]] (version 0.9.3, 2013-07-30)

This package should contain bafRegress.py and bafRegress.R

== About bafRegress ==

'''bafRegress''' is actually a pair of scripts, one Python (2.7) and one R. The Python script is the main interface and handles the parsing of Illumina final report files. The R script actually performs the regression model and provides the contamination estimates.

To use this program, you will need Final Report files from BeadStudio/GenomeStudio. You will need to have columns for the genotypes using the A/B Illumina coded alleles as well as the Illumina reported B allele frequency in addition to the standard sample/marker columns.

Additionally, you will also need allele frequency estimates for the markers on the genotype array. The file should have two columns: one with a marker name that matches the name in the Final Report file and another with the allele frequency for one of the two alleles with a value between 0.0-1.0 or NA if missing.

== Basic Usage ==

=== Processing Raw Final Report Files ===

If you have a final report file with exactly one sample in it, the most basic usage of the program is
$ python bafRegress.py estimate --freqfile popmaf.txt finalreport.txt > results.txt
The first parameter "estimate" tells the script you would like to estimate the level of contamination for the sample. You may specify as many Final Report files as you would like on the command line. By default, only the first sample in the file will be analyzed. The results are streamed to stdout, so be sure to redirect the output to a file.

If you have more than one sample per Final Report file, add the "--stacked" option
$ python bafRegress.py estimate --freqfile popmaf.txt --stacked finalreport.txt > results.txt

=== Processing Binary Files ===

Since Final Report files can be quite large and much of the work in the scripts is spend parsing the text files and only sending what is necessary to R to minimize memory usage. It can also be somewhat time consuming to repeatedly merge in the allele frequency data. Therefore we've also include an option to create binary data files which can be loaded and accessed much more quickly. This is especially true when there are multiple samples per file.

To convert a standard Final Report to a binary format, use
$ python bafRegress.py convert --outprefix mydata --freqfile popmaf.txt finalreport.txt
Here, a "--freqfile" is not required, but if provided, it will make merging the values during analysis much quicker. You may specify multiple Final Report files as arguments if you would like to merge them into the same binary format. The binary files will all start with the prefix specified by "--outprefix". Once created, you can test all the samples with
$ python bafRegress.py estimatebin mydata > results.txt
If you did not provide a "--freqfile" before, you may specify one at this step.

=== Final Report Options ===

Each of the actions "estimate","estimatebin", and "convert" also accept options for the different column names in the Final Report files. If your names to not match the expected names, you may override them. The options are

* --colsample=col, sample column [default: Sample Name]
* --colmarker=col, marker column [default: SNP Name]
* --colbaf=col, B allele frequency column [default: B Allele Freq]
* --colab1=col, AB Allele 1 column [default: Allele1 - AB]
* --colab2=col, AB Allele 2 column [default: Allele2 - AB]

=== Subset Options ===

If you would only like to include certain markers (or exclude certain markers) there are options to do that as well. (Note, when using binary files, you will only need to do this during the "convert" step.). These options happen to follow the same parameter names used by PLINK.

* --extract=FILE Include only these markers
* --exclude=FILE Include all but these markers
* --keep=FILE Include only these individuals
* --remove=FILE Include all but these individuals

By default these files are split by white space and the first column is used. The sample name or marker name must match exactly to what is in the Final Report. If you want to change the field separator or the column used for option "X", you may set "--Xcol" or "--Xsep" respectively (eg --extractsep="," or --keepcol=2)

=== Frequency File Options ===

A file with frequency information is needed for analsis. You can specify

*--freqfile=FILE, Text file with marker name and population frequency
*--freqcols=COLS, Columns for marker/frequency [default 1,2]
*--freqsep=SEP, Split FILE using this [default: white space]

You must specify two columns, the marker and the frequency (in that order). So if you use PLINK to calculate allele frequencies, you would specify "--freqcols=2,5". Also note that only the minor allele frequency is used, so if the frequency provided is >0.50, it is automatically reduced by 0.50 during analysis.

== Plotting ==

We're provided basic support for plotting samples if you would like to visually inspect them for anomalies as well. You would use
$ python bafRegress.py plot --freqfile popmaf.txt finalreport.txt
or
$ python bafRegress.py plotbin --sample SAMPLENAME mydata
depending on whether you are using the Final Report files or the binary versions.

Here is an example of the plot for an uncontaminated vs a contaminated sample. Note how the uncontaminated sample has values closer to the expected BAF of 0 and 1 for the homozygotes. Also note that in the contaminated sample, the deviance from the expected seems to increase as a function of the minor allele frequency (MAF).

[[File:Bafregressplotexample.gif]]

== Interpreting Results ==

For each sample, the following values are returned:

*estimate - This is the estimate of contamination from the model (on the 0.0-1.0 scale)
*stderr - The standard error of the estimate
*tval - The test statistic
*pval - The p-value of the estimate
*callrate - The call rate of the sample (number of non-missing genotypes)
*Nhom - The number of homozygous genotypes used to fit the model

You would typically set an estimate cutoff of 1%-2% as a lower bound. If you have many SNPs, sometimes the result can have a significant p-value but the detected level of contamination is like 0.2% which is practically insignificant. This regression method is effective at quantifying modest levels of contamination. More extreme levels of contamination are harder to estimate, but will have a dramatic effect on the call rate making it go way down. You'll probably want to set a minimum reasonable call rate threshold on the samples as well (say, 95%).

Finally, It is useful to look at Nhom to see how many markers were used to create the estimate. You'll want to make sure you're using at least 1,000 markers to get good estimates. With a typical genome-wide array, this shouldn't be a problem at all.

== Reference ==

Please cite the following paper:

G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang, ''Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data'', American journal of human genetics doi:10.1016/j.ajhg.2012.09.004 (volume 91 issue 5 pp.839 - 848)

User talk:Corbinq

2018-04-19T19:13:33Z

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User:Corbinq

2018-04-19T19:13:33Z

Mflick: Creating user page for new user.

I'm a PhD candidate in Biostatistics working with Mike Boehnke and Hyun Min Kang. My methodological interests include integrative modeling to identify molecular mechanisms underlying GWAS signals, causal inference, experimental design, and efficient computational methods for large and high-dimensional data sets. Before coming to Michigan, I worked as an undergraduate research assistant at the University of Kansas CRMDA.

User talk:Lefaivej

2018-04-19T19:12:48Z

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User:Lefaivej

2018-04-19T19:12:47Z

Mflick: Creating user page for new user.

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User talk:Nwakim

2017-11-15T15:45:31Z

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User:Nwakim

2017-11-15T15:45:31Z

Mflick: Creating user page for new user.

I am a grad student in Biostatistics. I am part of CSG and GSTP. The main purpose for requesting an account is so that I can add a presentation for biostat 866.
I graduated from the University of Virginia with a B.S. in Biomedical Engineering. I am currently pursuing a Masters in Biostatistics at the University of Michigan.

User talk:Jweinstk

2017-11-15T15:45:22Z

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User:Jweinstk

2017-11-15T15:45:22Z

Mflick: Creating user page for new user.

I am a graduate student in the University of Michigan biostatistics department as of 2016. I am a trainee in the Genome Science Training program and I work in Goncalo’s group. I received a BA in mathematics from Emory University in 2015. I previously worked as a statistical analyst before attending graduate school.

User talk:Bwolford

2017-11-15T15:45:07Z

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User:Bwolford

2017-11-15T15:45:07Z

Mflick: Creating user page for new user.

I am a student in BIOSTAT866 and we need to upload presentations for class. I am a 2nd year bioinformatics PhD student mentored by Dr. Mike Boehnke and Dr. Cristen Willer, so I am a Center for Statistical Genetics trainee. I am also on the Genome Science Training Program training grant.

User talk:Schanks

2017-11-15T15:44:51Z

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User:Schanks

2017-11-15T15:44:51Z

Mflick: Creating user page for new user.

I am a PhD student in the Department of Biostatistics (beginning Fall 2016) studying statistical genetics. I am a trainee on the Genome Sciences Training Grant and work with Mike Boehnke and Laura Scott, and am interested in studying the genetics of Type 2 Diabetes.
I have previously earned a B.A. in Mathematics and Statistics from Barnard College.

User talk:Abought

2017-11-15T15:43:46Z

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User:Abought

2017-11-15T15:43:46Z

Mflick: Creating user page for new user.

Applications Programmer / Analyst at Center for Statistical Genetics, University of Michigan. Joined June 2017.

Contributes to Genes for Good, LocusZoom.js, and other projects. PhD in Chemistry, various projects and various software languages as needed. Side interests in web application development and API design, usability / UX, open science/open data, etc.

CSG Tech Talks

2017-08-23T17:56:33Z

Mflick:

The Center for Statistical Genetics (CSG) is hosting a series of talks to help people working in the field of statistical genetics, or applied statistics in general, become more knowledgeable about the technical tools available to them.

We will be hosting meetings during the summer on alternating Wednesdays at 2pm at SPH2 (in room 1152 unless otherwise noted).

To be notified of upcoming presentations, you may add your e-mail address to the csg-tech-talks@umich.edu mailing list on [https://mcommunity.umich.edu MCommunity]

To suggest topic or volunteer to present, please email Matthew at mflick@umich.edu

== Upcoming Schedule ==

* Aug 23, 2pm -- SPH2 M1152 - '''Concurrency''' by Jonathon LeFaive [https://docs.google.com/presentation/d/1y-iLTPxYy25tjxmHtq14K-00IqXutDv84hzKOddSon8/edit?usp=sharing Slides]

== Presentation Slides ==

* [https://github.com/welchr/csg-snakemake/raw/master/materials/tech_talk_snakemake_20170726.pptx Make and Snakemake by Matthew Flickinger, Ryan Welch (July 26, 2017)] - [https://github.com/welchr/csg-snakemake Github]
* [[Media:Dplyr_tidyverse.pdf| dplyr and the tidyverse by Matthew Flickinger (July 12, 2017)]] -[https://gist.githubusercontent.com/MrFlick/4297321683f9b3d483a4303e5acd586e/raw/716e2668d483d21e402ddb33dd618168ec697fe0/dplyr_tidyverse.Rmd Markdown Document] - [[Media:Dplyr_tidyverse_md.pdf| Rendered Markdown]]
* [[Media:Cplusplus11-features-and-tricks.pdf| C++11 Features and Tricks by Daniel Taliun (Jul 28, 2016)]]
* [[Media:ReproducibleResearch-TechTalk.pdf| Reproducible Research by Matthew Flickinger (Jul 14, 2016)]]
* [[Media:Julia_presentation.pdf| The Julia Manifesto by Jonathon LeFaive (Jun 30, 2016)]]
* [https://github.com/welchr/csg-jupyter-tutorial Quick introduction to the jupyter notebook by Ryan Welch (Jun 02, 2016)]
* [[Media:TechTalk-RTroubleshooting.pdf| What R You Doing? (Answering Your Own R Questions) by Matthew Flickinger (May 19, 2016)]]
* [[Media:Brooksisms.ppt| Brookisms And Other Nuggets of Programming Wisdom by Chris Clark (May 12, 2016)]]

CSG Tech Talks

2017-08-23T14:08:18Z

Mflick:

The Center for Statistical Genetics (CSG) is hosting a series of talks to help people working in the field of statistical genetics, or applied statistics in general, become more knowledgeable about the technical tools available to them.

We will be hosting meetings during the summer on alternating Wednesdays at 2pm at SPH2 (in room 1152 unless otherwise noted).

To be notified of upcoming presentations, you may add your e-mail address to the csg-tech-talks@umich.edu mailing list on [https://mcommunity.umich.edu MCommunity]

To suggest topic or volunteer to present, please email Matthew at mflick@umich.edu

== Upcoming Schedule ==

* Aug 23, 2pm -- SPH2 M1152 - '''Concurrency''' by Jonathon LeFaive

== Presentation Slides ==

* [https://github.com/welchr/csg-snakemake/raw/master/materials/tech_talk_snakemake_20170726.pptx Make and Snakemake by Matthew Flickinger, Ryan Welch (July 26, 2017)] - [https://github.com/welchr/csg-snakemake Github]
* [[Media:Dplyr_tidyverse.pdf| dplyr and the tidyverse by Matthew Flickinger (July 12, 2017)]] -[https://gist.githubusercontent.com/MrFlick/4297321683f9b3d483a4303e5acd586e/raw/716e2668d483d21e402ddb33dd618168ec697fe0/dplyr_tidyverse.Rmd Markdown Document] - [[Media:Dplyr_tidyverse_md.pdf| Rendered Markdown]]
* [[Media:Cplusplus11-features-and-tricks.pdf| C++11 Features and Tricks by Daniel Taliun (Jul 28, 2016)]]
* [[Media:ReproducibleResearch-TechTalk.pdf| Reproducible Research by Matthew Flickinger (Jul 14, 2016)]]
* [[Media:Julia_presentation.pdf| The Julia Manifesto by Jonathon LeFaive (Jun 30, 2016)]]
* [https://github.com/welchr/csg-jupyter-tutorial Quick introduction to the jupyter notebook by Ryan Welch (Jun 02, 2016)]
* [[Media:TechTalk-RTroubleshooting.pdf| What R You Doing? (Answering Your Own R Questions) by Matthew Flickinger (May 19, 2016)]]
* [[Media:Brooksisms.ppt| Brookisms And Other Nuggets of Programming Wisdom by Chris Clark (May 12, 2016)]]

CSG Tech Talks

2017-08-17T20:31:23Z

Mflick: /* Upcoming Schedule */

The Center for Statistical Genetics (CSG) is hosting a series of talks to help people working in the field of statistical genetics, or applied statistics in general, become more knowledgeable about the technical tools available to them.

We will be hosting meetings during the summer on alternating Wednesdays at 2pm at SPH2 (in room 1152 unless otherwise noted).

To be notified of upcoming presentations, you may add your e-mail address to the csg-tech-talks@umich.edu mailing list on [https://mcommunity.umich.edu MCommunity]

To suggest topic or volunteer to present, please email Matthew at mflick@umich.edu

== Upcoming Schedule ==

* July 26, 2pm - SPH2 M1152 - '''Make and Snakemake''' by Matthew Flickinger, Ryan Welch
** [https://github.com/welchr/csg-snakemake/raw/master/materials/tech_talk_snakemake_20170726.pptx Slides]
** [https://github.com/welchr/csg-snakemake Github]
* Aug 23, 2pm -- SPH2 M1152 - '''Concurrency''' by Jonathon LeFaive

== Presentation Slides ==

* [[Media:Dplyr_tidyverse.pdf| dplyr and the tidyverse by Matthew Flickinger (July 12, 2017)]] -[https://gist.githubusercontent.com/MrFlick/4297321683f9b3d483a4303e5acd586e/raw/716e2668d483d21e402ddb33dd618168ec697fe0/dplyr_tidyverse.Rmd Markdown Document] - [[Media:Dplyr_tidyverse_md.pdf| Rendered Markdown]]
* [[Media:Cplusplus11-features-and-tricks.pdf| C++11 Features and Tricks by Daniel Taliun (Jul 28, 2016)]]
* [[Media:ReproducibleResearch-TechTalk.pdf| Reproducible Research by Matthew Flickinger (Jul 14, 2016)]]
* [[Media:Julia_presentation.pdf| The Julia Manifesto by Jonathon LeFaive (Jun 30, 2016)]]
* [https://github.com/welchr/csg-jupyter-tutorial Quick introduction to the jupyter notebook by Ryan Welch (Jun 02, 2016)]
* [[Media:TechTalk-RTroubleshooting.pdf| What R You Doing? (Answering Your Own R Questions) by Matthew Flickinger (May 19, 2016)]]
* [[Media:Brooksisms.ppt| Brookisms And Other Nuggets of Programming Wisdom by Chris Clark (May 12, 2016)]]

Regions of high linkage disequilibrium (LD)

2017-07-27T17:02:23Z

Mflick:

Regions of high linkage disequilibrium (LD)

2017-07-27T17:02:03Z

Mflick:

Regions of high linkage disequilibrium (LD)

2017-07-27T16:55:31Z

Mflick:

CSG Tech Talks

2017-07-26T17:51:58Z

Mflick: /* Upcoming Schedule */

The Center for Statistical Genetics (CSG) is hosting a series of talks to help people working in the field of statistical genetics, or applied statistics in general, become more knowledgeable about the technical tools available to them.

We will be hosting meetings during the summer on alternating Wednesdays at 2pm at SPH2 (in room 1152 unless otherwise noted).

To be notified of upcoming presentations, you may add your e-mail address to the csg-tech-talks@umich.edu mailing list on [https://mcommunity.umich.edu MCommunity]

To suggest topic or volunteer to present, please email Matthew at mflick@umich.edu

== Upcoming Schedule ==

* July 26, 2pm - SPH2 M1152 - '''Make and Snakemake''' by Matthew Flickinger, Ryan Welch
** [https://github.com/welchr/csg-snakemake/raw/master/materials/tech_talk_snakemake_20170726.pptx Slides]
** [https://github.com/welchr/csg-snakemake Github]
* Aug 23, 2pm -- Room TBD - '''Concurrency''' by Jonathon LeFaive

== Presentation Slides ==

* [[Media:Dplyr_tidyverse.pdf| dplyr and the tidyverse by Matthew Flickinger (July 12, 2017)]] -[https://gist.githubusercontent.com/MrFlick/4297321683f9b3d483a4303e5acd586e/raw/716e2668d483d21e402ddb33dd618168ec697fe0/dplyr_tidyverse.Rmd Markdown Document] - [[Media:Dplyr_tidyverse_md.pdf| Rendered Markdown]]
* [[Media:Cplusplus11-features-and-tricks.pdf| C++11 Features and Tricks by Daniel Taliun (Jul 28, 2016)]]
* [[Media:ReproducibleResearch-TechTalk.pdf| Reproducible Research by Matthew Flickinger (Jul 14, 2016)]]
* [[Media:Julia_presentation.pdf| The Julia Manifesto by Jonathon LeFaive (Jun 30, 2016)]]
* [https://github.com/welchr/csg-jupyter-tutorial Quick introduction to the jupyter notebook by Ryan Welch (Jun 02, 2016)]
* [[Media:TechTalk-RTroubleshooting.pdf| What R You Doing? (Answering Your Own R Questions) by Matthew Flickinger (May 19, 2016)]]
* [[Media:Brooksisms.ppt| Brookisms And Other Nuggets of Programming Wisdom by Chris Clark (May 12, 2016)]]

CSG Tech Talks

2017-07-24T17:40:05Z

Mflick:

The Center for Statistical Genetics (CSG) is hosting a series of talks to help people working in the field of statistical genetics, or applied statistics in general, become more knowledgeable about the technical tools available to them.

We will be hosting meetings during the summer on alternating Wednesdays at 2pm at SPH2 (in room 1152 unless otherwise noted).

To be notified of upcoming presentations, you may add your e-mail address to the csg-tech-talks@umich.edu mailing list on [https://mcommunity.umich.edu MCommunity]

To suggest topic or volunteer to present, please email Matthew at mflick@umich.edu

== Upcoming Schedule ==

* July 26, 2pm - SPH2 M1152 - '''Make and Snakemake''' by Ryan Welch

== Presentation Slides ==

* [[Media:Dplyr_tidyverse.pdf| dplyr and the tidyverse by Matthew Flickinger (July 12, 2017)]] -[https://gist.githubusercontent.com/MrFlick/4297321683f9b3d483a4303e5acd586e/raw/716e2668d483d21e402ddb33dd618168ec697fe0/dplyr_tidyverse.Rmd Markdown Document] - [[Media:Dplyr_tidyverse_md.pdf| Rendered Markdown]]
* [[Media:Cplusplus11-features-and-tricks.pdf| C++11 Features and Tricks by Daniel Taliun (Jul 28, 2016)]]
* [[Media:ReproducibleResearch-TechTalk.pdf| Reproducible Research by Matthew Flickinger (Jul 14, 2016)]]
* [[Media:Julia_presentation.pdf| The Julia Manifesto by Jonathon LeFaive (Jun 30, 2016)]]
* [https://github.com/welchr/csg-jupyter-tutorial Quick introduction to the jupyter notebook by Ryan Welch (Jun 02, 2016)]
* [[Media:TechTalk-RTroubleshooting.pdf| What R You Doing? (Answering Your Own R Questions) by Matthew Flickinger (May 19, 2016)]]
* [[Media:Brooksisms.ppt| Brookisms And Other Nuggets of Programming Wisdom by Chris Clark (May 12, 2016)]]

CSG Tech Talks

2017-07-12T15:59:02Z

Mflick:

The Center for Statistical Genetics (CSG) is hosting a series of talks to help people working in the field of statistical genetics, or applied statistics in general, become more knowledgeable about the technical tools available to them.

We will be hosting meetings during the summer on alternating Wednesdays at 2pm at SPH2 (in room 1152 unless otherwise noted).

To be notified of upcoming presentations, you may add your e-mail address to the csg-tech-talks@umich.edu mailing list on [https://mcommunity.umich.edu MCommunity]

To suggest topic or volunteer to present, please email Matthew at mflick@umich.edu

== Upcoming Schedule ==

* July 12, 2pm - SPH M1655 - '''dplyr and the tidyverse''' by Matthew Flickinger [[Media:Dplyr_tidyverse.pdf| slides]] -[https://gist.githubusercontent.com/MrFlick/4297321683f9b3d483a4303e5acd586e/raw/716e2668d483d21e402ddb33dd618168ec697fe0/dplyr_tidyverse.Rmd Markdown Document] - [[Media:Dplyr_tidyverse_md.pdf| Rendered Markdown]]
* July 26, 2pm - SPH2 M1152 - '''Make and Snakemake''' by Ryan Welch

== Presentation Slides ==

* [[Media:Cplusplus11-features-and-tricks.pdf| C++11 Features and Tricks by Daniel Taliun (Jul 28, 2016)]]
* [[Media:ReproducibleResearch-TechTalk.pdf| Reproducible Research by Matthew Flickinger (Jul 14, 2016)]]
* [[Media:Julia_presentation.pdf| The Julia Manifesto by Jonathon LeFaive (Jun 30, 2016)]]
* [https://github.com/welchr/csg-jupyter-tutorial Quick introduction to the jupyter notebook by Ryan Welch (Jun 02, 2016)]
* [[Media:TechTalk-RTroubleshooting.pdf| What R You Doing? (Answering Your Own R Questions) by Matthew Flickinger (May 19, 2016)]]
* [[Media:Brooksisms.ppt| Brookisms And Other Nuggets of Programming Wisdom by Chris Clark (May 12, 2016)]]