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ai-driver

AI-based prediction of driver mutations

bycom

methylcytosine calling (5mC calling) from BS-seq.

cellxgene_vip

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

epidenovo

A platform for linking regulatory de novo mutations to developmental epigenetics and diseases

imrep

ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.

inomics

Interpreting Nucleases Off-targeting by Modeling Integrated-data Combined with Sequence specificity in CRISPR–Cas9 system.

iupac-nucleotide-motif-search

IUPAC-nucleotide-motif-search

mbridge

Estimating genome-wide single-base methylation level from MB-seq data combined with RRBS data.

mec

Magic-Enzyme-Cutter：Magic-Enzyme-Cutter is a software that Master Restriction Enzyme II digestion in silico && Evaluate the degradation products in many aspects && Calculate the optimal selection in expect (MEC)

oncobase

A platform for decoding regulatory somatic mutations in human cancers

rbp-var

A platform for exploring functional variants involved in post-transcriptional regulation mediated by RNA-binding proteins

scrna-tools

Table of software for the analysis of single-cell RNA-seq data.

singlesplice

Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: http://nar.oxfordjournals.org/content/early/2016/01/05/nar.gkv1525.full

snakepipes

A toolkit based on snakemake and python for analysis of NGS data

sramap

Convert SRA data to mapped BAM/Bigwig/Bed in one step by parallel computation

xflicsu.github.io