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agat

Another Gtf/Gff Analysis Toolkit

alphafold

Open source code for AlphaFold.

anchorwave

sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

arcsv

Complex structural variant detection from WGS data

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

awesome-ggplot2

A curated list of awesome ggplot2 tutorials, packages etc.

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

awesome-vdj

📚 Tools and databases for analyzing HLA and VDJ genes.

bamnostic

a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool

bedtk

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

biostructmap

A Python package for mapping sequence aligned data onto protein structures

cartographs

ccsmeth

Detecting DNA methylation from PacBio CCS reads

chm13

Ultra-long reads for CHM13 genome assembly

circlize

Circular visualization in R

cnv_functionalannotation

cnvgram

Draw CNV diagrams

complex-upset

A library for creating complex UpSet plots with ggplot2 geoms

corshrink

R package for adaptive correlation and covariance matrix shrinkage.

d4-format

The D4 Quantatative Data Format

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

deeplearning-biology

A list of deep learning implementations in biology

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

deepsvp

Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity

dipcall

Reference-based variant calling pipeline for a pair of phased haplotype assemblies

doppelganger

Target site duplication assessment from alignment file and genomic location of insertion sites.

drawcell

R package to create cell pictures.

evmutation

Mutation effects predicted from sequence co-variation

fastbook

The fastai book, published as Jupyter Notebooks