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aml-training

The most recent version of the Applied Machine Learning notes

ashr

An R package for adaptive shrinkage

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

cdr3-qtl

Trans-association between HLA and TCR-CDR3

cell-type-ieqtl-pipeline

A collection of scripts to estimate cell type estimates from bulk tissue gene expression data, perform ieQTL mapping and run colocalization analysis

cheatsheets

RStudio Cheat Sheets

corrr

R package for exploring correlations

crop-seq

Repository for the processing and analysis of CROP-seq data

cropseq.analysis

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

dacor

data_manipulation_benchmarks

A set of data manipulation benchmarking code for Julia and R

dplyr-cli

Manipulate CSV files on the command line using dplyr

effective-computing

Effective Computing—Resources for Computational Biologists

eqtl-intro

An introductory course to eQTL analysis.

eqtlbma

Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fastq-bed-subset

Filter fastq file based on bed regions

fastqtl

Fork of FastQTL for SVs

finemapr

Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF

fiveminutestats

A repo of short "vignettes" illustrating statistical concepts

gtexresults

Code and data resources accompanying Urbut et al (2017), "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions."

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

hail

Scalable genomic data analysis.

imrep

ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.

locuscomparer

LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.

locuszoom-standalone

Create regional association plots from GWAS or meta-analysis

manhattan-plot-eqtls-per-gene

mashr

An R package for multivariate adaptive shrinkage.

mixedmodels-misc

miscellaneous materials for mixed models, mostly in R