Benjamin Fair's repositories
cookiecutter-wflowR-smk
cookiecutter template of workflowR combined with snakemake pipeline in code
design-mpeseq-primers
For designing RT primers with blast search, tm constraints, etc
GenometracksByGenotype
Helper script to plot molQTLs. Normalize and group bigwigs by genotype.
recurrent-splicing-identification
running leaf cutter from snaptron data to identify differential splice events, esp those associate with SF3B1
SmallMoleculeRNASeq
RNAseq analysis of small molecule splicing modifiers
dotfiles
dot files
snakemake-workflow_rna-seq
Basic RNA-seq snakemake workflow. Use as a module for larger workflows.
.vim
my .vim and vimrc
201907_mpe-seq_processing
align and deduplicate paired reads from MPE-seq protocol
align-reads-walkthrough
basic alignment commands for getting used to ngs processing on midway. mpe-seq data used as example.
apaQTL
Project for apaQTL MS
cheRNA_pilot
Exploratory analysis of chromatin enriched RNAs from LCLs
cola-seq_bp_calling
Snakemake pipeline for calling BPs from CoLa-see data
Comparative_eQTL
Primary data: Chimp eQTLs called from heart tissue samples
cookiecutter-pypackage
Cookiecutter template for a Python package.
eigenMT
An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants
example-rmd-templates
đź“„ A selection of minimal examples used to highlight R Markdown templates, as referred to in the "R Markdown Definitive Guide"
leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
pandoc_resume
The Markdown Resume
rna-seq-dhx38
Analysis of RNA-seq from ipsc derived neurons
rna-seq_simplequantification
snakemake workflowr project for basic RNA-seq processing
ScerSpliceSeq
Pipeline for aligning reads, counting splice junctions, and making plots of splice-seq data
snaptron-analysis
analysis of sf3b1 splicing
sQTL
pipeline i used for calling sQTL in chimps
YouCompleteMe
A code-completion engine for Vim