Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
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Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
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Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
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visual_genome_python_driverby ranjaykrishna
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Parameter/topology editor and molecular simulator
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Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
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Collections of library structure and sequence of popular single cell genomic methods
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A guided, intuitive introduction to genomics for software engineers. Curated by the community.
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R package for integrating and analyzing multiple single-cell datasets
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Fast Whole-Genome Similarity (ANI) Estimation
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GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
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🌈 Interactive analysis of metagenomics data
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Bayesian haplotype-based mutation calling
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Automatic and customizable compile time transformations between similar case classes and sealed traits/enums, essentially a thing that glues your code. Scala 3 only. Or is it duct 🤔
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Differential analysis of RNA-Seq
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Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
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avogadroby cryos
Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
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pyensemblby openvax
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
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Bismarkby FelixKrueger
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
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noodlesby zaeleus
Bioinformatics I/O libraries in Rust
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vcf2mafby mskcc
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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atlasby metagenome-atlas
ATLAS - Three commands to start analyzing your metagenome data
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medakaby nanoporetech
Sequence correction provided by ONT Research
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SARS-CoV-2_Sequencingby CDCgov
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
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cellphonedbby Teichlab
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strelkaby Illumina
Strelka2 germline and somatic small variant caller
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squidpyby scverse
Spatial Single Cell Analysis in Python
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biogoby biogo
biogo is a bioinformatics library for Go
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bioconvertby bioconvert
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
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FastQCby s-andrews
A quality control analysis tool for high throughput sequencing data
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NanoPlotby wdecoster
Plotting scripts for long read sequencing data
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atac-seq-pipelineby ENCODE-DCC
ENCODE ATAC-seq pipeline
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pySCENICby aertslab
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
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HiC-Proby nservant
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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visual_genome_python_driverby ranjaykrishna
A python wrapper for the Visual Genome API
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ParmEdby ParmEd
Parameter/topology editor and molecular simulator
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SpliceAIby Illumina
A deep learning-based tool to identify splice variants
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bionodeby bionode
Modular and universal bioinformatics
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baktaby oschwengers
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
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AGATby NBISweden
Another Gtf/Gff Analysis Toolkit
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plipby pharmai
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
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metaWRAPby bxlab
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
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NextDenovoby Nextomics
Fast and accurate de novo assembler for long reads
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RNAseq-workflowby twbattaglia
A repository for setting up a RNAseq workflow
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gatkby broadgsa
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
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scg_lib_structsby Teichlab
Collections of library structure and sequence of popular single cell genomic methods
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pyGenoby tariqdaouda
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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homebrew-bioby brewsci
:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
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learngenomics.devby stjude
A guided, intuitive introduction to genomics for software engineers. Curated by the community.
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ligerby welch-lab
R package for integrating and analyzing multiple single-cell datasets
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FastANIby ParBLiSS
Fast Whole-Genome Similarity (ANI) Estimation
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SCENICby aertslab
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
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gffreadby gpertea
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
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pavianby fbreitwieser
🌈 Interactive analysis of metagenomics data
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octopusby luntergroup
Bayesian haplotype-based mutation calling
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ducktapeby arainko
Automatic and customizable compile time transformations between similar case classes and sealed traits/enums, essentially a thing that glues your code. Scala 3 only. Or is it duct 🤔
Scala 280Updated: 2 y ago License: Proprietary (Proprietary)
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sleuthby pachterlab
Differential analysis of RNA-Seq
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MAGICby KrishnaswamyLab
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
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HIVIEWby openhisilicon
Open multi-process software framework for hisilicon (海思) ipc/dvr/nvr/ebox
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tutorialsby mmatschiner
Tutorials on phylogenetic and phylogenomic inference
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SURVIVORby fritzsedlazeck
Toolset for SV simulation, comparison and filtering
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brain_segmentationby naldeborgh7575
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qiimeby biocore
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Python 272Updated: 4 y ago License: Strong Copyleft (GPL-2.0)
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CheckMby Ecogenomics
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
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pdb-toolsby haddocking
A dependency-free cross-platform swiss army knife for PDB files.
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training-materialby galaxyproject
A collection of Galaxy-related training material
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