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action

Archetypal analysis for Cell Type identificatION (ACTION)

anchor

This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge

awesome-multi-omics

List of software packages for multi-omics analysis

awesome-nextflow

A curated list of nextflow based pipelines

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

awesome-single-cell

List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

awosome-bioinformatics

A curated list of resources for learning bioinformatics.

baseqdrops

A versatile and lightning fast package for processing 10X, inDrop and Drop-seq data.

bat-cochlea

Study the molecular mechanism of mammalian hearing frequency variation

bbknn

Batch balanced KNN

bigscale

An Analytical Framework for Big-Scale Single Cell Data

bigscale2

Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data

bismark

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

bitmapperbs

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing

bs3

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

cardelino

casper

cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data

cellbench_data

This contains the dataset for comparing scRNA-seq analysis methods

cellfishing.jl

Fast and scalable cell search tool

cellphonedb

cellrouter

Reconstruction of complex single-cell trajectories using CellRouter

cellsius

CellSIUS: Cell Subtype Identification from Upregulated gene Sets

cemitool

Co-Expression Module Identification Tool (CEMiTool) official repository

cerebra

high-throughput summarizing of vcf entries following a sequencing experiment

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

chipseeker

:dart:ChIP peak Annotation, Comparison and Visualization

chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

chisel

CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links