hj1994412's repositories
AGAT
Another Gff Analysis Toolkit
arxiv-sanity-preserver
Web interface for browsing, search and filtering recent arxiv submissions
eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
flair
Full-Length Alternative Isoform analysis of RNA
GAAS
Genome Assembly and Annotation Service code
gffcompare
classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
gffread
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
ggClusterNet
Microbial ecological network visualization clustering
HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
HuaSmallTools
Some bioinformic domestic scripts.
karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
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
MakeHub
Fully automated generation of UCSC assembly hubs
MicrobiomeStatPlot
Interpretation and visualization of microbiome charts
minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
msfs_teo
mSFS using a teosinte natural population
NINJA
Nearly Infinite Neighbor Joining Application
phast
PHAST
pseudoRef
Make Pseudo-Reference Genome from VCF/BCF
pychopper
A tool to identify, orient, trim and rescue full length cDNA reads
rstantools
Tools for Developing R Packages Interfacing with Stan
sra-tools
SRA Tools
STAR-Fusion
STAR-Fusion codebase
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms