doaneas Goto Github PK

dotfiles

:wrench: .files, including ~/.macos — sensible hacker defaults for macOS

elementoepigenomics

fishhook

R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

fripflow

nextflow pipeline to calculate atac-seq frip scores from processed bam files

gatk

GATK 4beta singularity

genomation

R package for genomic feature analysis and visualization

genomescale_scripts

scripts I use for making genome-scale transcriptional regulatory networks

ggnome

R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework

ggthemes

ggplot themes and scales

grape-nf

An automated RNA-seq pipeline using Nextflow

gsea_r

Updated implementation of the GSEA-P R application for modern R distributions

gtrack

R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework

gxg

Scalable GenomicRanges based class for storing, manipulating, and querying genomic matrices and pairwise features.

h2o-tutorials

Tutorials and training material for the H2O Machine Learning Platform

hic-pro

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

homerkit

Read HOMER motif analysis output in R.

iheatmapr

Complex, interactive heatmaps in R

io-2012-slides

Automatically exported from code.google.com/p/io-2012-slides

ipython-contrib

IPython-contrib is an unofficial organisation that try to regroup project that are made to be used with IPython. Please ask if you want to add a project !

ipython-in-depth

IPython in-depth Tutorial, first presented at PyCon 2012

jp_gene_viz

A collection of visualizations for genomics related information for use with Jupyter notebooks.

juicebox

Software for visualizing data from Hi-C and other proximity mapping experiments

juicebox-1

Visualization and analysis software for Hi-C data -

junctionseq

The JunctionSeq R package is a powerful tool for testing differential junction usage (DJU) in next-generation, high-throughput RNA-Seq experiments.

jupyter-docker-stacks

Opinionated stacks of ready-to-run Jupyter applications in Docker. Forked to add GPU capabilities.

khtools

R package for misc tools

libevent

A public libevent repository. The official repository is at https://github.com/libevent/libevent

lowrankmodels.jl

LowRankModels.jl is a julia package for modeling and fitting generalized low rank models.

mintscripts

collection of scripts for mint-ChIP processing

mskilibs