Scientific Software
Updated 9 months ago

khmer release v2.1 — Peer-reviewed • Rank 18.9 • Science 100%

khmer release v2.1: software for biological sequence analysis - Published in JOSS (2017)

Scientific Software
Updated 9 months ago

Nextclade — Peer-reviewed • Rank 14.3 • Science 95%

Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)

Scientific Software
Updated 9 months ago

restez — Peer-reviewed • Rank 11.0 • Science 93%

restez: Create and Query a Local Copy of GenBank in R - Published in JOSS (2018)

Scientific Software · Peer-reviewed
Scientific Software
Updated 9 months ago

oxDNA — Peer-reviewed • Rank 7.9 • Science 95%

oxDNA: coarse-grained simulations of nucleic acids made simple - Published in JOSS (2023)

Biology (40%)
Scientific Software · Peer-reviewed
Updated 9 months ago

adapt-diagnostics • Rank 9.5 • Science 75%

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

Updated 9 months ago

biopython • Rank 32.2 • Science 49%

Official git repository for Biopython (originally converted from CVS)

Updated 9 months ago

hlatyping • Rank 7.2 • Science 67%

Precision HLA typing from next-generation sequencing data

Updated 9 months ago

qslib • Rank 10.0 • Science 64%

QSLib is a package for interacting with Applied Biosystems' QuantStudio qPCR machines, intended for non-qPCR uses, such as DNA computing and molecular programming systems.

Updated 9 months ago

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.

Updated 9 months ago

pyfaidx • Rank 23.0 • Science 49%

Efficient pythonic random access to fasta subsequences

Updated 9 months ago

biomarkovchains.jl • Rank 3.4 • Science 64%

Representing biological sequences as Markov chains

Updated 9 months ago

snps • Rank 15.8 • Science 46%

tools for reading, writing, merging, and remapping SNPs

Updated 9 months ago

open3spn2 • Rank 9.2 • Science 49%

An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM

Updated 9 months ago

dnacurve • Rank 7.3 • Science 49%

DNA curvature analysis.

Updated 9 months ago

pyfastx • Rank 18.1 • Science 36%

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Updated 9 months ago

kevlar • Rank 5.3 • Science 41%

Reference-free variant discovery in large eukaryotic genomes

Updated 9 months ago

https://github.com/bowang-lab/bioreason • Rank 5.8 • Science 36%

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model

Updated 9 months ago

lineage • Rank 14.5 • Science 26%

tools for genetic genealogy and the analysis of consumer DNA test results

Updated 9 months ago

aroma.affymetrix • Rank 12.5 • Science 23%

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

Updated 9 months ago

fluentdna • Rank 9.0 • Science 13%

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Updated 9 months ago

https://github.com/biojulia/bio.jl • Rank 11.1 • Science 10%

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Updated 9 months ago

https://github.com/broadinstitute/genepy • Rank 8.9 • Science 10%

Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python

Updated 9 months ago

primer3plus • Rank 8.5 • Science 10%

A easy-to-use Python API for Primer3 primer design.

Updated 9 months ago

oncoanalyser • Science 57%

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Updated 9 months ago

https://github.com/ciaranomara/bedgraph.jl • Science 23%

Read and write support for bedGraph file format.

Updated 9 months ago

SimpleBio • Science 54%

Easy-to-use biological sequence tools working with DNA, RNA and aminoacid sequences.

Updated 9 months ago

modle • Science 67%

High-performance stochastic modeling of DNA loop extrusion interactions

Updated 9 months ago

catch • Science 75%

A package for designing compact and comprehensive capture probe sets.

Updated 9 months ago

https://github.com/biomedsciai/geno4sd • Science 13%

An python omics data toolkit for the analysis across biological scales

Updated 9 months ago

https://github.com/brentp/falas • Science 13%

Fragment-Aware Local Assembly for Short-reads

Updated 9 months ago

qdna • Science 67%

QuantumDNA is an open-source Python package for simulating exciton and charge transfer in DNA using quantum mechanical methods. Designed for interdisciplinary research, it combines a user-friendly GUI with efficient tools for statistical screening of DNA sequences.

Updated 9 months ago

sammyseq • Science 67%

Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

Updated 9 months ago

bcdatabaser • Science 41%

A pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data

Updated 9 months ago

Shiny-WGCNA • Science 49%

Shiny app for WGCNA for RNAseq and DNA methylation data

Updated 9 months ago

TwistMethylFlow • Science 67%

A NextFlow pipeline for Twist NGS DNA Methylation data analysis

Updated 9 months ago

intro_to_dna_data_publishing • Science 44%

An introductory course for publishing DNA to GBIF, using the Darwin Core standard.

Updated 9 months ago

https://github.com/const-ae/neural_network_dna_demo • Science 13%

Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction