hj1994412's repositories
BioData
All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
bioinformatics_train
虽然喜欢做湿实验，但是开始了生信的学习之路
clinker
Gene cluster comparison figure generator
CompareM
A toolbox for comparative genomics.
ggClusterNet
Microbial ecological network visualization clustering
graftM
GraftM - Rapid community profiles from metagenomes
GToTree
A user-friendly workflow for phylogenomics
icn3d
web-based protein structure viewer and analysis tool interactively or in batch mode
inStrain
Bioinformatics program inStrain
kent
UCSC Genome Browser source tree. Stable branch: "beta".
MACSE_V2_PIPELINES
This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.
maffilter
The MafFilter genome alignment processor
msfs_teo
mSFS using a teosinte natural population
phast
PHAST
phylo
Helper scripts for making phylogenies
pseudoRef
Make Pseudo-Reference Genome from VCF/BCF
rgeos
:exclamation: This is a read-only mirror of the CRAN R package repository. rgeos — Interface to Geometry Engine - Open Source ('GEOS'). Homepage: https://r-forge.r-project.org/projects/rgeos/ https://libgeos.org http://rgeos.r-forge.r-project.org/index.html
social_niche_breadth_SNB
Calculate the Social Niche Breadth (SNB) score of all taxonomic lineages in a set of microbiomes.
topic-functional-annotation
A repository for the lessons and notebooks used for Binder tutorials
treedater
Scalable relaxed clock phylogenetic dating
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms