ivivek87's repositories
GenVisR
Genome data visualizations
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
RSkittleBrewer
for those times you want to make plots with candy-themed color schemes
fishplot
Create timecourse "fish plots" that show changes in the clonal architecture of tumors
UpSetR
An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
epic
diffuse domain ChIP-Seq caller based on SICER
AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
STAR
RNA-seq aligner
bioinformatics-cafe
Unsorted scripts for bioinformatics. Former google.code bioinformatics-misc
methylkit
Automatically exported from code.google.com/p/methylkit
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
SICERpy
Python wrapper around the popular ChIP-Seq peak caller SICER
oneliners
Useful bash one-liners for bioinformatics.
bpipe
Bpipe - a tool for running and managing bioinformatics pipelines
bioinformatics-hacks
A collection of Python scripts I use for random bioinformatics-related tasks.
work_setup
Different workstation related setups
pysam
Automatically exported from code.google.com/p/pysam
PARE
PARE: a computational method to Predict Active Regulatory Elements
picardmetrics
:vertical_traffic_light: Run Picard and collate multiple metrics.
HaveYouSwappedYourSamples
This project contains simple methods to measure sample relatedness and identify potential swaps and contamination
SciRNotebook
Template for building a lab notebook using RMarkdown
tximport
Import and summarize transcript-level estimates for gene-level analysis
TS
Torrent Suite
rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
systemPipeR
NGS workflow environment
Perl-for-Bioinformatics
An attempt to help anyone interested in using Perl for Bioinformatics
ubu
UNC-Chapel Hill Bioinformatics Utilities
DEGandMore
Analyses related to differential gene expression and functional annotation