This is a tool that will take a group of HCP data files that are tarred by subject and extract data files and subjects from the full dataset.
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An ImageJ plugin to analyze the flagellar beat of sperm, motile cilia beat, and sperm steering.
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Simulates a sequence including: The Recaman Sequence
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Short, reproducible phylogenomic cuts
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Files_For_Creating_sh-Extracting_databy GithubYueJian
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2 Version:Current
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License: No License (No License)This repository includes files that can create command line file for HM and can extract data from txt files
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In-development script for identifying chimeric transcripts in a de novo assembled transcriptome
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Single-cell RNA-seq analysis
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PISPINO (PIpits SPIN-Off tools): Bioinformatics toolkits for processing NGS data
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Python 2 Version:Current License: No License (No License)
License: No License (No License)Biomedical Citation Selector Trainer
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A Python script and UI designed to create submission files for HTCondor
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Proteins Binding Site Finder
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CLI for splitting a fastq that has multiple readgroups
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Concise gene descriptions generator
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mid file to mbseq (Microbrute sequence) converter
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A Python package for genomics
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Convert GFF, fastas, annotation table and species name into Genbank.
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A tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA
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pangenome Functional Enrichment Analysis from Roary
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Variant calling + processing pipline using GATK based in Snakemake
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Tools to analyze mailing list data
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Pipeline for analysing M. tuberculosis nanopore reads and getting drug susceptibility information.
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extra pumped heatmaps
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Survey analysis (Estimation of genomic characteristics) for plant and animal de novo genome projects
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Process FASTA format sequences
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Python version of CRISPRcleanR: An R package for unsupervised identification and correction of gene independent cell responses to CRISPR-cas9 targeting
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This is a script to download Sanger sequencing data from University of Michigan sequencing core.
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Python script to parse blast files and assign each read to the taxonomic of the lowest common ancestor
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A Python package for clustering of single nucleotide variants from high-through seqencing data.
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De novo transcriptome analysis pipeline using Snakemake workflow manager
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SARS-CoV-2_Northern_California_genomic_surveillanceby laduplessis
Python 2 Version:Current License: No License (No License)
License: No License (No License)Data used for analyses in "Genomic Surveillance Reveals Multiple Introductions of SARS-CoV-2 into Northern California" (Deng et al., Science, 2020) https://doi.org/10.1126/science.abb9263
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Insect identification
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Bioinformatic sequence analysis of membrane proteins
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Combine a set of metagenomic assemblies into a common set of references
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clinical reseach genome scripts
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The program Hydrocluster is designed to determine the position, size and content of hydrophobic, hydrophilic and charged clusters in protein molecules. The program is based on the DBSCAN algorithm.
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Cabbage looper
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A web application to analyze the genome sequence of known or unknown viruses and predict its potential target organs in the human body.
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Differential Evolution algorithm
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Phylogenetic analyses of SARS-CoV-2 proteins
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HPV-EM is an HPV genotyping tool that utilizes an expectation maximization algorithm to identify the presence of HPV genotypes in a sample from RNA-seq data
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Nucleotide (DNA/RNA) sequence to a protein sequence translation tool
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A set of scripts for looking piRNA guide-target pairs by integrating small RNA-seq and degradome-seq data
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Bucket-based Compression of Bacterial Genome Sequencing Data with Dynamic de Bruijn Graph
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A Python 3 library to visualize Bioinformatics, Computational Biology and Medical Informatics data
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hcp_extraction_toolby shots47s
This is a tool that will take a group of HCP data files that are tarred by subject and extract data files and subjects from the full dataset.
Python 2Updated: 5 y ago License: No License (No License)
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SpermQby hansenjn
An ImageJ plugin to analyze the flagellar beat of sperm, motile cilia beat, and sperm steering.
Java 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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sequence-simulator-javaby AbdullahRasheed
Simulates a sequence including: The Recaman Sequence
Java 2Updated: 3 y ago License: No License (No License)
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SARS-CoV-2-heterogeneityby elkebir-group
Python 2Updated: 3 y ago License: No License (No License)
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ortholangby jefdaj
Short, reproducible phylogenomic cuts
Python 2Updated: 3 y ago License: Strong Copyleft (AGPL-3.0)
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Files_For_Creating_sh-Extracting_databy GithubYueJian
This repository includes files that can create command line file for HM and can extract data from txt files
Python 2Updated: 3 y ago License: No License (No License)
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ChimeraKillerby masonaj157
In-development script for identifying chimeric transcripts in a de novo assembled transcriptome
Python 2Updated: 4 y ago License: No License (No License)
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scRNAby JurijsNazarovs
Single-cell RNA-seq analysis
Python 2Updated: 4 y ago License: No License (No License)
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pispinoby hsgweon
PISPINO (PIpits SPIN-Off tools): Bioinformatics toolkits for processing NGS data
Python 2Updated: 6 y ago License: No License (No License)
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biomedical-citation-selector-trainerby ncbi
Biomedical Citation Selector Trainer
Python 2Updated: 4 y ago License: No License (No License)
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condor-submit-creatorby deppen8
A Python script and UI designed to create submission files for HTCondor
Python 2Updated: 3 y ago License: Permissive (MIT)
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Site-Finderby mfawzysami
Proteins Binding Site Finder
Python 2Updated: 4 y ago License: No License (No License)
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gdc-fastq-splitterby kmhernan
CLI for splitting a fastq that has multiple readgroups
Python 2Updated: 4 y ago License: Permissive (Apache-2.0)
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a
agr_genedescriptionsby alliance-genome
Concise gene descriptions generator
Python 2Updated: 2 y ago License: Permissive (MIT)
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midi2mbseqby mebitek
mid file to mbseq (Microbrute sequence) converter
Java 2Updated: 3 y ago License: Permissive (Apache-2.0)
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scikit-genomeby scikit-genome
A Python package for genomics
Python 2Updated: 3 y ago License: No License (No License)
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gff_to_gbkby ArnaudBelcour
Convert GFF, fastas, annotation table and species name into Genbank.
Python 2Updated: 3 y ago License: Permissive (MIT)
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coreuscanby kristyhoran
A tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA
Python 2Updated: 3 y ago License: No License (No License)
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GearRecOutby lipingfangs
Python 2Updated: 4 y ago License: No License (No License)
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GemSpotby mjrober101
Python 2Updated: 4 y ago License: Strong Copyleft (AGPL-3.0)
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panFEARby DrQuestion
pangenome Functional Enrichment Analysis from Roary
Python 2Updated: 4 y ago License: Permissive (MIT)
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r
rnaseq-variant-gatkby samleenz
Variant calling + processing pipline using GATK based in Snakemake
Python 2Updated: 4 y ago License: Permissive (MIT)
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mailingListAnalysisby gaalcaras
Tools to analyze mailing list data
Python 2Updated: 4 y ago License: No License (No License)
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Longitude_pipelineby mbhall88
Pipeline for analysing M. tuberculosis nanopore reads and getting drug susceptibility information.
Python 2Updated: 4 y ago License: No License (No License)
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u
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survey_oldby bitcometz
Survey analysis (Estimation of genomic characteristics) for plant and animal de novo genome projects
Python 2Updated: 3 y ago License: No License (No License)
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toolsby PGPHarvard
Python 2Updated: 6 y ago License: Proprietary (Proprietary)
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imputation-pipelineby ryhui
Python 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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SequenceProcessingby ToHanwei
Process FASTA format sequences
Python 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)Support
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pyCRISPRcleanRby cancerit
Python version of CRISPRcleanR: An R package for unsupervised identification and correction of gene independent cell responses to CRISPR-cas9 targeting
Python 2Updated: 4 y ago License: Strong Copyleft (GPL-3.0)
2Updated: 4 y ago License: Strong Copyleft (GPL-3.0)Support
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SangUMby azdaly
This is a script to download Sanger sequencing data from University of Michigan sequencing core.
Python 2Updated: 4 y ago License: No License (No License)
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blast_getLCAby frederikseersholm
Python script to parse blast files and assign each read to the taxonomic of the lowest common ancestor
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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V
VarClustby fasterius
A Python package for clustering of single nucleotide variants from high-through seqencing data.
Python 2Updated: 3 y ago License: Proprietary (Proprietary)
2Updated: 3 y ago License: Proprietary (Proprietary)Support
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dntapby arnaudmeng
De novo transcriptome analysis pipeline using Snakemake workflow manager
Ruby 2Updated: 4 y ago License: No License (No License)
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SARS-CoV-2_Northern_California_genomic_surveillanceby laduplessis
Data used for analyses in "Genomic Surveillance Reveals Multiple Introductions of SARS-CoV-2 into Northern California" (Deng et al., Science, 2020) https://doi.org/10.1126/science.abb9263
Python 2Updated: 4 y ago License: No License (No License)
2Updated: 4 y ago License: No License (No License)Support
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i
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korbinianby teese
Bioinformatic sequence analysis of membrane proteins
Python 2Updated: 6 y ago License: No License (No License)
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integrate-metagenomic-assembliesby FredHutch
Combine a set of metagenomic assemblies into a common set of references
Python 2Updated: 3 y ago License: Permissive (MIT)
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hydroclusterby alashkov83
The program Hydrocluster is designed to determine the position, size and content of hydrophobic, hydrophilic and charged clusters in protein molecules. The program is based on the DBSCAN algorithm.
Python 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)Support
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c
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predictoby TheWizard25
A web application to analyze the genome sequence of known or unknown viruses and predict its potential target organs in the human body.
Python 2Updated: 4 y ago License: No License (No License)
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ChIP-seqby wkl1990
Python 2Updated: 6 y ago License: No License (No License)
2Updated: 6 y ago License: No License (No License)Support
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differential_evolutionby cnlinxi
Differential Evolution algorithm
Python 2Updated: 4 y ago License: No License (No License)
2Updated: 4 y ago License: No License (No License)Support
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SARS-CoV-2-ProtPhylosby labbces
Phylogenetic analyses of SARS-CoV-2 proteins
Python 2Updated: 3 y ago License: No License (No License)
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HPV-EMby jin-wash-u
HPV-EM is an HPV genotyping tool that utilizes an expectation maximization algorithm to identify the presence of HPV genotypes in a sample from RNA-seq data
Python 2Updated: 3 y ago License: No License (No License)
2Updated: 3 y ago License: No License (No License)Support
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dSeq2pSeqby manushadilan
Nucleotide (DNA/RNA) sequence to a protein sequence translation tool
Python 2Updated: 4 y ago License: Strong Copyleft (GPL-3.0)
2Updated: 4 y ago License: Strong Copyleft (GPL-3.0)Support
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GTBusterby weng-lab
A set of scripts for looking piRNA guide-target pairs by integrating small RNA-seq and degradome-seq data
Python 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)Support
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BdBGby rongjiewang
Bucket-based Compression of Bacterial Genome Sequencing Data with Dynamic de Bruijn Graph
Python 2Updated: 5 y ago License: Permissive (MIT)
2Updated: 5 y ago License: Permissive (MIT)Support
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biovizby nandor-poka
A Python 3 library to visualize Bioinformatics, Computational Biology and Medical Informatics data
Python 2Updated: 4 y ago License: Strong Copyleft (GPL-3.0)
2Updated: 4 y ago License: Strong Copyleft (GPL-3.0)Support
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