rakarnik Goto Github PK

azimuth

Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency

bamtools

C++ API & command-line toolkit for working with BAM data

bioconda-recipes

Conda recipes for the bioconda channel.

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bs3

BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.

bsmap

Unofficial repo for software vendoring or packaging purposes

chia-pet2

a versatile and flexible pipeline for analysing different variants of ChIA-PET data

crispresso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

diffloop

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/diffloop.html Contributions: https://github.com/aryeelab/diffloop. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=diffloop or https://github.com/aryeelab/diffloop/issues.

gem3

GEM software suite (GEM, GPS, KMAC, KSM, RMD, etc.)

gsea-desktop

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

hic-pro

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

hichipper

A preprocessing and QC pipeline for HiChIP data

homebrew-games

:video_game: Games formulae for the Homebrew package manager

micc

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

moabs

A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data

motifspec

MotifSpec, a discriminative motif finder

origami

Statistical Modeling of ChIA-PET interactions

phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

rakarnik.github.io

rose

scanmot

Scan sequences for motif instances

scantop

Find top instances of motif in each sequence of a set of sequences

seurat

R toolkit for single cell genomics

sleuth

Differential analysis of RNA-Seq