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aiediting

bowtie

An ultrafast memory-efficient short read aligner

cutrun_tools

datasciencecoursera

datasciencecoursera

datasharing

The Leek group guide to data sharing

docker-homer

fork of the quay.io homer image, moving annotations to my hardcoded link

dplyr

Plyr specialised for data frames: faster & with remote datastores

fithichip

Statistically Significant loops from HiChIP data

frip

scripts for fRIP data analysis

hello-world

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hicup

Hi-C data processing pipeline

iread

iread

macs

MACS -- Model-based Analysis of ChIP-Seq

maps

micc

MICC: an R package for identifying chromatin interactions from ChIA-PET data

nmf

NMF: A Flexible R package for Nonnegative Matrix Factorization

pgltools

Paired Genomic Loci Tool Suite

plyr

A R package for splitting, applying and combining large problems into simpler problems

rentrez

talk with NCBI entrez using R

rnaseqana

rpubmed

Tools for extracting and processing Pubmed and Pubmed Central records.

sc_seq

single_cell_tools

seurat

R toolkit for single cell genomics

star_cuff

Use star and cufflinks for RNA seq data analysis

umi-grinder

The use of UMIs for sequencing becomes more and more frequently used so we need to take them into consideration when deduplicating data aligning to the same positions