ChIP-seq analysis notes from Ming Tang
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Jupyter widget to interactively view molecular structures and trajectories
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🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
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De novo assembler for single molecule sequencing reads using repeat graphs
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The next version of bwa-mem
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Python library to facilitate genome assembly, annotation, and comparative genomics
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Python library to handle Gene Ontology (GO) terms
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A single molecule sequence assembler for genomes large and small.
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Tools to process and analyze deep sequencing data.
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Embeddable genomic visualization component based on the Integrative Genomics Viewer
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Free open-source photogrammetry software tools
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awesome-genome-visualizationby cmdcolin
TypeScript 
566 Version:Current
License: No License (No License)
License: No License (No License)A list of interesting genome browser or genome-browser-like implementations
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Layout is a rust library and a tool that renders Graphviz dot files.
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SPAdes Genome Assembler
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The second version of the Kraken taxonomic sequence classification system
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Near-optimal RNA-Seq quantification
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Versatile open-source tool for microbiome analysis
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Phylogenetic orthology inference for comparative genomics
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Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
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Biostar Q&A
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Plant phenotyping with image analysis
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:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
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C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
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A fast and sensitive gapped read aligner
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A Go package for engineering organisms.
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Tools for working with generic types
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Easy alignment of multiple selections and multi-line selections
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Incubator for useful bioinformatics code, primarily in Python and R
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a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
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Raw nanopore signal mapper that enables real-time targeted sequencing
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phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
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MACS -- Model-based Analysis of ChIP-Seq
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Signal-level algorithms for MinION data
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BWK awk modified for biological data
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:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
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Ultra-fast and memory-efficient (meta-)genome assembler
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cBioPortal for Cancer Genomics
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hybrid assembly pipeline for bacterial genomes
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R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
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Open-source bioinformatics components for Dash
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Fast genome-wide functional annotation through orthology assignment
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A tool to find sequencing data and metadata from public databases.
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Cutadapt removes adapter sequences from sequencing reads
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JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
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Inferring CNV from Single-Cell RNA-Seq
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Remote protein homology detection suite.
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Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
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Gene cluster comparison figure generator
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Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
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Tools for handling Unique Molecular Identifiers in NGS data sets
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ChIP-seq-analysisby crazyhottommy
ChIP-seq analysis notes from Ming Tang
Python 645Updated: 11 mo ago License: Permissive (MIT)
645Updated: 11 mo ago License: Permissive (MIT)Support
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nglviewby nglviewer
Jupyter widget to interactively view molecular structures and trajectories
Jupyter Notebook 643Updated: 1 y ago License: Proprietary (Proprietary)
643Updated: 1 y ago License: Proprietary (Proprietary)Support
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salmonby COMBINE-lab
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
C++ 621Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
621Updated: 1 y ago License: Strong Copyleft (GPL-3.0)Support
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Flyeby fenderglass
De novo assembler for single molecule sequencing reads using repeat graphs
C 616Updated: 11 mo ago License: Proprietary (Proprietary)
616Updated: 11 mo ago License: Proprietary (Proprietary)Support
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bwa-mem2by bwa-mem2
The next version of bwa-mem
C++ 605Updated: 11 mo ago License: Proprietary (Proprietary)
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jcviby tanghaibao
Python library to facilitate genome assembly, annotation, and comparative genomics
Python 587Updated: 11 mo ago License: Permissive (BSD-2-Clause)
587Updated: 11 mo ago License: Permissive (BSD-2-Clause)Support
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goatoolsby tanghaibao
Python library to handle Gene Ontology (GO) terms
Python 582Updated: 1 y ago License: Permissive (BSD-2-Clause)
582Updated: 1 y ago License: Permissive (BSD-2-Clause)Support
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canuby marbl
A single molecule sequence assembler for genomes large and small.
C++ 575Updated: 1 y ago License: No License (No License)
575Updated: 1 y ago License: No License (No License)Support
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deepToolsby deeptools
Tools to process and analyze deep sequencing data.
Python 574Updated: 10 mo ago License: Proprietary (Proprietary)
574Updated: 10 mo ago License: Proprietary (Proprietary)Support
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igv.jsby igvteam
Embeddable genomic visualization component based on the Integrative Genomics Viewer
JavaScript 570Updated: 10 mo ago License: Permissive (MIT)
570Updated: 10 mo ago License: Permissive (MIT)Support
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micmacby micmacIGN
Free open-source photogrammetry software tools
C++ 568Updated: 10 mo ago License: Proprietary (Proprietary)
568Updated: 10 mo ago License: Proprietary (Proprietary)Support
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awesome-genome-visualizationby cmdcolin
A list of interesting genome browser or genome-browser-like implementations
TypeScript 566Updated: 10 mo ago License: No License (No License)
566Updated: 10 mo ago License: No License (No License)Support
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layoutby nadavrot
Layout is a rust library and a tool that renders Graphviz dot files.
Rust 564Updated: 10 mo ago License: Permissive (MIT)
564Updated: 10 mo ago License: Permissive (MIT)Support
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kraken2by DerrickWood
The second version of the Kraken taxonomic sequence classification system
C++ 551Updated: 11 mo ago License: Permissive (MIT)
551Updated: 11 mo ago License: Permissive (MIT)Support
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kallistoby pachterlab
Near-optimal RNA-Seq quantification
C 550Updated: 11 mo ago License: Permissive (BSD-2-Clause)
550Updated: 11 mo ago License: Permissive (BSD-2-Clause)Support
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vsearchby torognes
Versatile open-source tool for microbiome analysis
C++ 550Updated: 1 y ago License: Proprietary (Proprietary)
550Updated: 1 y ago License: Proprietary (Proprietary)Support
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OrthoFinderby davidemms
Phylogenetic orthology inference for comparative genomics
Python 549Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)
549Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)Support
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igvby igvteam
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
Java 547Updated: 11 mo ago License: Permissive (MIT)
547Updated: 11 mo ago License: Permissive (MIT)Support
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plantcvby danforthcenter
Plant phenotyping with image analysis
Python 542Updated: 10 mo ago License: Permissive (MIT)
542Updated: 10 mo ago License: Permissive (MIT)Support
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biojavaby biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Java 531Updated: 11 mo ago License: Weak Copyleft (LGPL-2.1)
531Updated: 11 mo ago License: Weak Copyleft (LGPL-2.1)Support
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vcflibby vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
C++ 529Updated: 1 y ago License: Permissive (MIT)
529Updated: 1 y ago License: Permissive (MIT)Support
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bowtie2by BenLangmead
A fast and sensitive gapped read aligner
C++ 528Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)
528Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)Support
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polyby TimothyStiles
A Go package for engineering organisms.
Go 515Updated: 10 mo ago License: Permissive (MIT)
515Updated: 10 mo ago License: Permissive (MIT)Support
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typetoolsby jhalterman
Tools for working with generic types
Java 513Updated: 3 y ago License: Permissive (Apache-2.0)
513Updated: 3 y ago License: Permissive (Apache-2.0)Support
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sublime_alignmentby wbond
Easy alignment of multiple selections and multi-line selections
Python 512Updated: 3 y ago License: No License (No License)
512Updated: 3 y ago License: No License (No License)Support
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bcbbby chapmanb
Incubator for useful bioinformatics code, primarily in Python and R
Python 502Updated: 3 y ago License: No License (No License)
502Updated: 3 y ago License: No License (No License)Support
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Bandageby rrwick
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
C++ 501Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
501Updated: 1 y ago License: Strong Copyleft (GPL-3.0)Support
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UNCALLEDby skovaka
Raw nanopore signal mapper that enables real-time targeted sequencing
C++ 498Updated: 1 y ago License: Permissive (MIT)
498Updated: 1 y ago License: Permissive (MIT)Support
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phyloseqby joey711
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
R 496Updated: 11 mo ago License: No License (No License)
496Updated: 11 mo ago License: No License (No License)Support
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MACSby macs3-project
MACS -- Model-based Analysis of ChIP-Seq
Python 488Updated: 3 y ago License: Permissive (BSD-3-Clause)
488Updated: 3 y ago License: Permissive (BSD-3-Clause)Support
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nanopolishby jts
Signal-level algorithms for MinION data
C++ 487Updated: 11 mo ago License: Permissive (MIT)
487Updated: 11 mo ago License: Permissive (MIT)Support
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bioawkby lh3
BWK awk modified for biological data
C 476Updated: 3 y ago License: No License (No License)
476Updated: 3 y ago License: No License (No License)Support
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DnaFeaturesViewerby Edinburgh-Genome-Foundry
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
Python 474Updated: 11 mo ago License: Permissive (MIT)
474Updated: 11 mo ago License: Permissive (MIT)Support
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megahitby voutcn
Ultra-fast and memory-efficient (meta-)genome assembler
C++ 474Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)
474Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)Support
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cbioportalby cBioPortal
cBioPortal for Cancer Genomics
Java 470Updated: 10 mo ago License: Strong Copyleft (AGPL-3.0)
470Updated: 10 mo ago License: Strong Copyleft (AGPL-3.0)Support
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Unicyclerby rrwick
hybrid assembly pipeline for bacterial genomes
C++ 464Updated: 11 mo ago License: Strong Copyleft (GPL-3.0)
464Updated: 11 mo ago License: Strong Copyleft (GPL-3.0)Support
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CellChatby sqjin
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
R 463Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)
463Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)Support
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dash-bioby plotly
Open-source bioinformatics components for Dash
Python 462Updated: 1 y ago License: Permissive (MIT)
462Updated: 1 y ago License: Permissive (MIT)Support
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eggnog-mapperby eggnogdb
Fast genome-wide functional annotation through orthology assignment
Python 461Updated: 10 mo ago License: Strong Copyleft (AGPL-3.0)
461Updated: 10 mo ago License: Strong Copyleft (AGPL-3.0)Support
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ffqby pachterlab
A tool to find sequencing data and metadata from public databases.
Python 460Updated: 11 mo ago License: Permissive (MIT)
460Updated: 11 mo ago License: Permissive (MIT)Support
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cutadaptby marcelm
Cutadapt removes adapter sequences from sequencing reads
Python 444Updated: 11 mo ago License: Permissive (MIT)
444Updated: 11 mo ago License: Permissive (MIT)Support
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jbrowseby GMOD
JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
JavaScript 444Updated: 10 mo ago License: Proprietary (Proprietary)
444Updated: 10 mo ago License: Proprietary (Proprietary)Support
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infercnvby broadinstitute
Inferring CNV from Single-Cell RNA-Seq
R 444Updated: 10 mo ago License: Proprietary (Proprietary)
444Updated: 10 mo ago License: Proprietary (Proprietary)Support
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hh-suiteby soedinglab
Remote protein homology detection suite.
C 440Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)
440Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)Support
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wtdbg2by ruanjue
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
C 429Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
429Updated: 3 y ago License: Strong Copyleft (GPL-3.0)Support
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clinkerby gamcil
Gene cluster comparison figure generator
Python 424Updated: 1 y ago License: Permissive (MIT)
424Updated: 1 y ago License: Permissive (MIT)Support
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edlibby Martinsos
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
C++ 423Updated: 1 y ago License: Permissive (MIT)
423Updated: 1 y ago License: Permissive (MIT)Support
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UMI-toolsby CGATOxford
Tools for handling Unique Molecular Identifiers in NGS data sets
Python 422Updated: 11 mo ago License: Permissive (MIT)
422Updated: 11 mo ago License: Permissive (MIT)Support
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