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bachu-mahe

Config files for my GitHub profile.

bashoneliners

A collection of practical or just pure awesome bash one-liners or shell script tips and tricks for GNU Linux, UNIX or BSD systems. Open, collaborative system, user friendly, with functions to contribute one-liners, request one-liners, search, rss feed, commenting, Open ID login. Open-source project, using Django, Python, jQuery, HTML5, Bootstrap from Twitter.

bc

Template for Software Carpentry bootcamp site repository.

bioc-refcard

Bioconductor cheat sheet

chip-pipeline

My Custom Snakemake ChIP-Seq Pipeline

chip-seq-pipeline

ChIP-Seq Pipeline implemented using Nextflow

chipseqfpro

ChIPSeqFPro (beta) is a script for full processing of ChIPSeq data starting from fastq files. It performs fastqc quality control, mapping to the human genome hg19 or mouse mm10 using bwa, sam to bam conversion, peak calling with MACS, creates bigwig files from bam files using bam2bigwig.

complexheatmap

make complex heatmaps as well as self define annotation graphics

datasciencecoursera

my first repository

datasharing

The Leek group guide to data sharing

dea.r

Script to automate differential expression analysis using DESeq2, edgeR or limma-voom

degust

A web tool for visualising differential gene expression data

deseq2

dgeclust

Hierarchical Non-Parametric Bayesian Clustering of Digital Expression Data

ergatis

Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines.

gephi

trunk

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

labs

Scripts for HarvardX courses: PH525x

ngs_short_cuts

oneliners

Useful bash one-liners for bioinformatics.

projects

In-progress projects at Harvard School of Public Health Bioinformaitcs Core

r-scripts

rnaseq

Tools for RNASeq analysis take file from SRA file to Fastq, run QC, map to genome and find DE genes.

shell-novice

Software Carpentry introduction to the shell for novices.

shell-scripts

Shell scripts for basic ChIP-Seq analysis

test-repo

usebioconductor

Training material for intermediate R / Bioconductor courses