graphsim — Peer-reviewed • Rank 14.3 • Science 98%

graphsim: An R package for simulating gene expression data from graph structures of biological pathways - Published in JOSS (2020)

TipToft — Peer-reviewed • Rank 8.3 • Science 100%

TipToft: detecting plasmids contained in uncorrected long read sequencing data - Published in JOSS (2019)

Multilocus sequence typing by blast from de novo assemblies against PubMLST — Peer-reviewed • Rank 6.1 • Science 100%

Multilocus sequence typing by blast from de novo assemblies against PubMLST - Published in JOSS (2016)

Pynteny — Peer-reviewed • Rank 6.4 • Science 98%

Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases - Published in JOSS (2023)

org.biojava • Rank 22.4 • Science 77%

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

higlass • Rank 18.2 • Science 77%

Fast, flexible and extensible genome browser.

cooler • Rank 17.7 • Science 77%

A cool place to store your Hi-C

bioframe • Rank 17.3 • Science 77%

Genomic interval operations on Pandas DataFrames

gosling.js • Rank 13.7 • Science 77%

Grammar of Scalable Linked Interactive Nucleotide Graphics

NGLess • Rank 13.9 • Science 75%

NGLess: NGS with less work

gget • Rank 20.2 • Science 67%

🧬 gget enables efficient querying of genomic reference databases

cazy-webscraper • Rank 9.9 • Science 77%

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

mudata • Rank 18.6 • Science 67%

Multimodal Data (.h5mu) implementation for Python

biocommons.seqrepo • Rank 18.1 • Science 67%

non-redundant, compressed, journalled, file-based storage for biological sequences

adapt-diagnostics • Rank 9.5 • Science 75%

A package for designing activity-informed nucleic acid diagnostics for viruses.

jcvi • Rank 16.7 • Science 67%

Python library to facilitate genome assembly, annotation, and comparative genomics

OpenOmics — Peer-reviewed • Rank 6.7 • Science 77%

OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. - Published in JOSS (2021)

bactmap • Rank 6.2 • Science 77%

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

cool-seq-tool • Rank 13.6 • Science 67%

pybbi • Rank 12.7 • Science 67%

Python bindings to UCSC BigWig and BigBed library

sarek • Rank 10.9 • Science 67%

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

arvados • Rank 23.1 • Science 54%

An open source platform for managing and analyzing biomedical big data

GEOquery • Rank 23.0 • Science 54%

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

trviz • Rank 9.7 • Science 67%

A python library for decomposing and visualizing tandem repeat sequences

nplinker • Rank 11.4 • Science 64%

A python framework for microbial natural products data mining by integrating genomics and metabolomics data

poppunk • Rank 7.5 • Science 67%

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

msprime • Rank 19.3 • Science 54%

Simulate genealogical trees and genomic sequence data using population genetic models

filtersam • Rank 6.3 • Science 67%

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

ncbi-genome-download • Rank 19.2 • Science 54%

Scripts to download genomes from the NCBI FTP servers

circdna • Rank 5.4 • Science 67%

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

xpressplot • Rank 4.7 • Science 67%

A toolkit for navigating and analyzing gene expression datasets

zol • Rank 7.1 • Science 62%

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

genbankpy • Rank 1.8 • Science 67%

Tools to download, parse and filter GenBank files

smoove • Rank 14.7 • Science 54%

structural variant calling and genotyping with existing tools, but, smoothly.

phables • Rank 10.4 • Science 57%

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

bedops • Rank 11.9 • Science 54%

:microscope: BEDOPS: high-performance genomic feature operations

staramr • Rank 11.7 • Science 54%

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

cnr-flow • Rank 1.6 • Science 64%

CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

divbrowse • Rank 6.6 • Science 57%

A web application for interactive visualization and exploratory data analysis of variant call matrices

circrna • Rank 6.1 • Science 57%

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

jvarkit • Rank 9.0 • Science 54%

Java utilities for Bioinformatics

ezaai • Rank 5.9 • Science 57%

EzAAI - High Throughput Prokaryotic AAI Calculator

kgp • Rank 8.6 • Science 54%

1000 Genomes Project Metadata R Package

pycirclize • Rank 16.1 • Science 44%

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

data-management-resources • Rank 2.7 • Science 57%

Repo supporting the manuscript 'Journeying towards best practice data management in biodiversity genomics'.

sns • Rank 4.2 • Science 54%

Analysis pipelines for genomic sequencing data

pymsaviz • Rank 13.9 • Science 44%

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

pygenomeviz • Rank 13.8 • Science 44%

A genome visualization python package for comparative genomics

recognizer • Rank 3.4 • Science 54%

A tool for domain based annotation with databases from the Conserved Domains Database

cogclassifier • Rank 8.4 • Science 44%

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

pybarrnap • Rank 7.2 • Science 44%

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

kevlar • Rank 5.3 • Science 41%

Reference-free variant discovery in large eukaryotic genomes

wrangling-genomics • Science 67%

Data Wrangling and Processing for Genomics

curationpretext • Science 65%

A Nextflow DSL2 pipeline for pretext generation in curation

bachelor_thesis • Science 44%

Bachelor Thesis

nthash • Science 44%

Fast hash function for DNA/RNA sequences

amr • Science 75%

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

variantcalling • Science 65%

Nextflow DSL2 pipeline to call variants on long read alignment.

lsabgc-pan • Science 75%

lsaBGC - suite for pan-BGC-omics analysis

seqinspector • Science 44%

QC pipeline to inspect your sequences

kmer-counter • Science 44%

Count kmers with a more efficient (faster) hash table

ensemblgenedownload • Science 65%

Nextflow DSL2 pipeline to download gene annotations from Ensembl.

genome_updater • Science 67%

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

hmnfusion • Science 67%

A tool to aggregate results of fusion produced by Genefuse and Lumpy and calculate allelic frequency

insdcdownload • Science 65%

Nextflow DSL2 pipeline to download assemblies from INSDC.

assemblebac • Science 67%

avantonder/assembleBAC is a bioinformatics best-practise analysis pipeline for assembling and annotating bacterial genomes.

genomeassembly • Science 75%

Implementation of ToL genome assembly workflows

readmapping • Science 65%

Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.

genealignment • Science 65%

An NF-core pipeline to alignment genesets against a given reference genome.

phanta • Science 67%

Illumina short read assembly data pipeline for phage

phunky • Science 67%

Nanopore long read assembly data pipeline for phage genomes

snakemake_rnaseq • Science 57%

A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)

veba • Science 67%

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

hipiler • Science 44%

Visual exploration of large genome interaction matrices with interactive small multiples.

phaseimpute • Science 44%

A bioinformatics pipeline to phase and impute genetic data

ufcg • Science 57%

UFCG: Universal Fungal Core Genes

rich_directrna • Science 57%

Nanopore directRNA (hopefully cDNA too ;)) workflow with many transcript reconstruction alternatives

hictkpy • Science 67%

Python bindings for hictk: read and write .cool and .hic files directly from Python

hictk • Science 67%

Blazing fast toolkit to work with .hic and .cool files

shell-genomics • Science 67%

Introduction to the Command Line for Genomics

scgdb-data • Science 18%

SCGDB®-Data: A manually curated dedicated schizosaccharomyces comparative genome database.

catch • Science 75%

A package for designing compact and comprehensive capture probe sets.

recimap • Science 44%

Recimap (a reciprocal mapping tool) was developed as a bioinformatics command-line tool/pipeline to find rearrangements breakpoints between two closely related genomes.

llfsrnaseq • Science 54%

An R package which stores the code used to process Long Life Family Study RNA sequencing from fastq to analysis releases

nf-core-scgs • Science 67%

Single Cell Genome Sequencing data analysis pipeline

chemcpa • Science 62%

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

mdeepfri • Science 75%

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

nplinker-webapp • Science 44%

The NPLinker web app, built with Plotly Dash, for visualizing NPLinker predictions

fetch_ngs • Science 67%

Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.

upimapi • Science 54%

UniProt Id Mapping through API

vcfx • Science 44%

VCFX is a collection of specialized C/C++ command-line tools designed for efficient manipulation, analysis, and transformation of VCF files.

tabula-rasa-website • Science 44%

Source code for Tabula Rasa lab website

computationalgenomicsmanual • Science 67%

Robs manual for the computational genomics and bioinformatics class.

rseb • Science 67%

An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.

ensemblrepeatdownload • Science 65%

Nextflow DSL2 pipeline to download repeat annotations from Ensembl.

StabilitySort • Science 41%

Stability Sort: detect instability

hictkr • Science 57%

R bindings for hictk: read .cool and .hic files directly from R

somalier • Science 67%

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

2024-04-25-rutgers • Science 18%

Genomics Carpentries Workshop at Rutgers University, April 25-26, 2024

islandevolution.github.io • Science 44%

Source code for the Island biology, diversification, genome evolution lab