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fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

feature-viewer-typescript

Library to visualize protein sequence features in Typescript using D3. This repository is based on calipho-sib/feature-viewer.

fishhook

R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

gggenomes

A grammar of graphics for comparative genomics

ggpubr

'ggplot2' Based Publication Ready Plots

ggstream

A package to make streamplots

gnomad_qc

gos

A declarative library for Python designed to create interactive multi-scale visualizations of genomics and epigenomics data.

graphia

A visualisation tool for the creation and analysis of graphs

green-varan

Annotate non-coding regulatory vars using our GREEN-DB, prediction scores, conservation and pop AF

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

hbcgm_paper

codes used in HbCGM_paper

hic_tools

A collection of tools for Hi-C data analysis

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

hificnv

Copy number variant caller and depth visualization utility for PacBio HiFi reads

hmftools

Various algorithms for analysing genomics data

imavirus

iris

A module for improving the insertion sequences of structural variant calls

jabba

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.

janggu

Deep learning infrastructure for bioinformatics

jigv

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

kinaction

Kinase in action.

long-read-catalog

catalog for long-read sequencing tools

long-rna-seq-pipeline

STAR based ENCODE Long RNA-Seq processing pipeline

lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.

lrrnaseqvariantcalling

Codes for the Iso-Seq variant-calling paper

metbrewer

Color palette package in R inspired by works at the Metropolitan Museum of Art in New York

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

missingno

Missing data visualization module for Python.

ml-genomics-resources

Machine Learning for Genomics and Therapeutics Resources (Cell Patterns)