Pinned Repositories
acfs
A pipeline for de novo circRNA identification
AmpliconArchitect
AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GrCH37 reference sequence and one or more regions of interest. This is development version. Please "watch" this repository for production release and methods manuscript soon.
analysis-workflows
MGI's Analysis Workflows and Pipelines managed by the BGA group.
angularplasmid
DNA Plasmid Visualization Component using AngularJS
Anime4K
A High-Quality Real Time Upscaler for Anime Video
ARACNe-AP
Network Reverse Engineering through AP inference of Mutual Information
asprintf.c
asprintf() implementation
atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
BayesPrism
a fully Bayesian approach to deconvolve tumor microenvironment
bedtools2-cygwin
A powerful toolset for genome arithmetic.
jchenpku's Repositories
jchenpku/bedtools2-cygwin
A powerful toolset for genome arithmetic.
jchenpku/BayesPrism
a fully Bayesian approach to deconvolve tumor microenvironment
jchenpku/AutoCAT
jchenpku/bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
jchenpku/CATT
An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.
jchenpku/chatgpt-prompts-for-academic-writing
This list of writing prompts covers a range of topics and tasks, including brainstorming research ideas, improving language and style, conducting literature reviews, and developing research plans.
jchenpku/chiptk
optimized protocol for processing 50-bp SE ChIP-seq
jchenpku/ChromosomeMappings
This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
jchenpku/ComBat-seq
Batch effect adjustment based on negative binomial regression for RNA sequencing count data
jchenpku/DGSEA
jchenpku/docker-jdownloader-2
Docker container for JDownloader 2
jchenpku/DriverML
DriverML identifies cancer driver genes. Rigorous and unbiased benchmark analysis and comparisons of DriverML with 20 other existing tools in 31 independent datasets from The Cancer Genome Atlas (TCGA) show that DriverML is robust and powerful among various datasets and outperforms the other tools with a better balance of precision and recall.
jchenpku/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
jchenpku/gatk-sv
A structural variation pipeline for short-read sequencing
jchenpku/gridss
GRIDSS: the Genomic Rearrangement IDentification Software Suite
jchenpku/HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
jchenpku/hmftools
Various utility tools for working with genomics data
jchenpku/htslib
C library for high-throughput sequencing data formats
jchenpku/immunarch
immunarch: An R Package for Painless Bioinformatics Analysis of T-cell and B-cell Immune Repertoire Data
jchenpku/immunedeconv
A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)
jchenpku/metaWRAP
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
jchenpku/OncoSig
Code to run OncoSig Analyses
jchenpku/parallel-fastq-dump
parallel fastq-dump wrapper
jchenpku/qupath
QuPath - Open Source Digital Pathology
jchenpku/rmappet
Nextflow pipeline for performing parallel alternative splicing analysis using rMATS and Whippet and then overlapping the results.
jchenpku/samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
jchenpku/scRNAseq_analysis_vignette
Tutorial for scRNA-seq data analysis beginners using R
jchenpku/SingleR
SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
jchenpku/statrethinking_winter2019
Statistical Rethinking course at MPI-EVA from Dec 2018 through Feb 2019
jchenpku/superFreq
Analysis pipeline for cancer exomes