khmer release v2.1
khmer release v2.1: software for biological sequence analysis - Published in JOSS (2017)
Nextclade
Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)
oxDNA
oxDNA: coarse-grained simulations of nucleic acids made simple - Published in JOSS (2023)
adapt-diagnostics
A package for designing activity-informed nucleic acid diagnostics for viruses.
biopython
Official git repository for Biopython (originally converted from CVS)
qslib
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.
circdna
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.
open3spn2
An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM
https://github.com/broadinstitute/gatk
Official code repository for GATK versions 4 and up
https://github.com/bowang-lab/bioreason
BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model
lineage
tools for genetic genealogy and the analysis of consumer DNA test results
aroma.affymetrix
🔬 R package: Analysis of Large Affymetrix Microarray Data Sets
fluentdna
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.
https://github.com/biojulia/bio.jl
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
https://github.com/broadinstitute/genepy
Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python
https://github.com/ciaranomara/bedgraph.jl
Read and write support for bedGraph file format.
SimpleBio
Easy-to-use biological sequence tools working with DNA, RNA and aminoacid sequences.
https://github.com/biomedsciai/geno4sd
An python omics data toolkit for the analysis across biological scales
qdna
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.
sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
bcdatabaser
A pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data
TwistMethylFlow
A NextFlow pipeline for Twist NGS DNA Methylation data analysis
intro_to_dna_data_publishing
An introductory course for publishing DNA to GBIF, using the Darwin Core standard.
https://github.com/const-ae/neural_network_dna_demo
Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction
https://github.com/bioinformaticsfmrp/bioc2017.tcgabiolinks.elmer
Integrative analysis workshop with TCGAbiolinks and ELMER