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awesome-deepbio

A curated list of awesome deep learning applications in the field of computational biology

bis-tools

A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )

blotter

bedford lab research

circlize

Circular visualization in R

complexheatmap

make complex heatmaps as well as self define annotation graphics

d3e

Discrete Distributional Differential Expression

dmrcate-devel

devel git for DMRcate

docker-test

elmer

Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes

enrichedheatmap

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.

gtrellis

Genomic plot in trellis layout

long-rna-seq-pipeline

STAR based ENCODE Long RNA-Seq processing pipeline

rgreat

Client for GREAT Analysis

scrna.seq.course

Analysis of single cell RNA-seq data course, Cambridge University, UK

scrna.seq.datasets

Collection of public scRNA-Seq datasets used by our group

sesame

R package for analyzing Infinium DNA methylation BeadChip data