xingsiyuan Goto Github PK

bamaddrg

adds sample names and read-group (RG) tags to BAM alignments

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

bin

bioinformatics

Code

cheatsheets

RStudio Cheat Sheets

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js

fastqc

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

gatk

Official code repository for GATK versions 4 and up

hello-world

My own Public Repository

hiblup

:surfer: HIBLUP is an Integration of Statistical Methods Under BLUP Framework for Genomic Selection and Prediction

impulsede

ImpulseDE

iterativewgcna

Extension of the WGCNA program to improve the eigengene similarity of modules and increase the overall number of genes in modules.

lncpipe

A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

masigpro

minimac4

ngstools

piblup

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).

poplddecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

python

All Algorithms implemented in Python

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

shiny_cuffdiff

Shiny code to interrogate cuffdiff databases and make plots on the basis of gene names and XLOC numbers

star

RNA-seq aligner

star-fusion

STAR-Fusion codebase

vadt

VADT_3.0.0 New and Improved

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.