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Statistics course for JHU Genomic Data Science Sequence
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A genotype query interface.
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Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
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data and model repository for single-cell data
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R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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Detect and visualize target mutations by scanning FastQ files directly
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“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
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SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
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:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
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MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
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cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
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Code examples of fast and simple k-mer counters for tutorial purposes
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BLASR: The PacBio® long read aligner
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A SingleCell RNASeq pre-processing snakemake workflow
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polymodelling toolset
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ichorCNAby broadinstitute
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
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lancetby nygenome
Microassembly based somatic variant caller for NGS data
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SEEDby baoe
Efficient clustering of next generation sequences
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Bioinformatics-Workshopsby gladstone-institutes
Workshops presented by the Gladstone Bioinformatics Core
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Palantirby dpeerlab
Single cell trajectory detection
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Ragoutby fenderglass
Chromosome-level scaffolding using multiple references
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biofx_pythonby kyclark
Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)
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dittoSeqby dtm2451
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
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Biostat-578by raphg
A repository for all of my teaching material
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pyprocarby romerogroup
A Python library for electronic structure pre/post-processing
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genstatsby jtleek
Statistics course for JHU Genomic Data Science Sequence
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benchmarking-toolsby ga4gh
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
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pythonby albertlauncher
A repository for the official Python extensions
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circlatorby sanger-pathogens
A tool to circularize genome assemblies
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truvariby spiralgenetics
Structural variant toolkit for VCFs
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SingleRby LTLA
Clone of the Bioconductor repository for the SingleR package.
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psmcby lh3
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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FLASby baoe
Fast and High Throughput Algorithm for PacBio Long Read Self-Correction
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pdbtoolsby harmslab
A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files
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ComputationalGenomicsManualby linsalrob
Robs manual for the computational genomics and bioinformatics class.
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GAASby NBISweden
Genome Assembly and Annotation Service code
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readfqby lh3
Fast multi-line FASTA/Q reader in several programming languages
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Exomiserby exomiser
A Tool to Annotate and Prioritize Exome Variants
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VirSorter2by jiarong
customizable pipeline to identify viral sequences from (meta)genomic data
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pymrmrby fbrundu
Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
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chemfilesby chemfiles
Library for reading and writing chemistry files
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annotablesby stephenturner
R data package for annotating/converting Gene IDs
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ReMILOby songc001
Reference Assisted Misassembly Detection Algorithm Using Short and Long Reads
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pydnaby BjornFJohansson
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
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pyGenomeVizby moshi4
A genome visualization python package for comparative genomics
Python 128Updated: 2 y ago License: Permissive (MIT)
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shinyCircosby YaoLab-Bioinfo
an R/shiny application for creation of Circos plot interactively
HTML 128Updated: 3 y ago License: No License (No License)
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gcp-variant-transformsby googlegenomics
GCP Variant Transforms
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weblogoby WebLogo
WebLogo 3: Sequence Logos redrawn
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sfairaby theislab
data and model repository for single-cell data
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pagoda2by kharchenkolab
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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MutScanby OpenGene
Detect and visualize target mutations by scanning FastQ files directly
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MASTby RGLab
Tools and methods for analysis of single cell assay data in R
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HiCPlotterby kcakdemir
“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
Python 126Updated: 4 y ago License: No License (No License)
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SigProfilerExtractorby AlexandrovLab
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Python 126Updated: 2 y ago License: Permissive (BSD-2-Clause)
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metaGEMby franciscozorrilla
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Python 126Updated: 2 y ago License: Permissive (MIT)
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METABOLICby AnantharamanLab
A scalable high-throughput metabolic and biogeochemical functional trait profiler
Perl 126Updated: 2 y ago License: No License (No License)
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metaeukby soedinglab
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
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cisTopicby aertslab
cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
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kmer-cntby lh3
Code examples of fast and simple k-mer counters for tutorial purposes
C++ 126Updated: 4 y ago License: Permissive (MIT)
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blasrby PacificBiosciences
BLASR: The PacBio® long read aligner
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dropSeqPipeby Hoohm
A SingleCell RNASeq pre-processing snakemake workflow
R 126Updated: 4 y ago License: Strong Copyleft (CC-BY-SA-4.0)
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scRNAtoolVisby junjunlab
Useful functions to make your scRNA-seq plot more cool!
R 126Updated: 2 y ago License: Proprietary (Proprietary)
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JD-Miter-Boxby JohnKazucki
polymodelling toolset
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SALSAby marbl
SALSA: A tool to scaffold long read assemblies with Hi-C data
Python 125Updated: 4 y ago License: Permissive (MIT)
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