This script takes in a tab-separated file containing at least one column of Ensembl IDs and a string indicating the header for this column, and outputs a tab-separated file identical to the input file except that it has an additional column containing mapped HGNC gene symbols for each row.
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An adjacency graph visualisation of protein interaction data.
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A flexible tool to identify mobile genetic elements and their sites of insertions from short-read whole-genome sequencing data.
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Generate two phased Juicebox .assembly files from one master .assembly for FALCON-Phase
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MHC binding analysis to define protein immune orthogonality. See Moreno et al. 2018.
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MARVEL: Metagenomic Analyses and Retrieval of Viral Elements
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A package to process, analyze, and interpret data from frequency-resolved X-ray absorption spectroscopy measurements.
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kmer-extract-by-trigger-siteby Comai-Lab
Python 
2 Version:Current License: Strong Copyleft (AGPL-3.0)
A script for extracting kmers (k base pair sized words) from fastq sequencing files after a specific trigger sequence.
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Provides static analysis, transformation, and code generation mechanisms in an extensible set of programming languages
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server development routine worker
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My own tools for protein structure
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viral KMER enrichment - Used to enrich viral reads in an input dataset
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BSc Senior Project, Bioinformatics Django web platform for storage and analysis of Biological data. Still in use by the group CHROMEVOL from FIU
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dna-alignment-jfarris587by IUDataStructuresCourse
Java 2 Version:Current
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License: No License (No License)dna-alignment-jfarris587 created by GitHub Classroom
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Use this to search for any protein in the NCBI Database, align it to a reference sequence, and build a concensus sequence.
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Recent studies discovered a widespread induction of transcriptional readthrough as a consequence of various stress conditions in mammalian cells. This novel phenomenon, initially identified from the analysis of RNA-seq data, suggests intriguing new levels of gene expression regulation. However, the mechanism underlying the readthrough phenomenon, as well as its regulatory consequences, still remain elusive. Furthermore, the readthrough response to stress has thus far not been investigated outside of mammalian species, and the occurrence of the readthrough phenomenon in many physiological and disease conditions remains to be explored. To facilitate a wider investigation into transcriptional readthrough, we created the DoGFinder software, which allows the identification and quantification of readthrough transcripts, DoGs, from any RNA-seq dataset. We further used DoGFinder to discover DoG induction in human PME cells following hypoxia – a previously unknown readthrough inducing stress type. This python based freely available software will enable users to explore, in a few simple steps, the readthrough phenomenon in any condition and organism.
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Tools for finding and working with structural representations of DNA motifs.
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Snakemake workflow for the vg toolkit.
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Metagenomics pipeline for human diet analysis using organelles genomes
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Clustering-mRNA-Expression-Databy abishpius
Python 2 Version:Current License: No License (No License)
License: No License (No License)Example of clustering mRNA expression data from the Cancer Cell Line Database.
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selectable_pkg_variants_exampleby jjhelmus
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Cath protein structure classification sets
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Assignment project 2. Identification of gene regulatory network from gene expression time-course data
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Helper scripts for bcbio-nextgen
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plot genome track data (for example from a BigWig file)
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Compare package dependencies across all your repositories
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DNA Curvature Analysis. Forked from https://pypi.org/project/dnacurve
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Converting Codon Sequences to Corresponding Acid Sequences.
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Misc JACK-related tools
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A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.
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From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)
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Supporting information for the paper "DNA shape complements sequence-based representations of transcription factor binding sites"
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Make Ramachandran plots from pdb files
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NER-of-Experimental-Facilitiesby ljwmusclenlper
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Gexplora - user-interface to analyse genomic elements along chromosomes
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GAT (Generic Genome-Wide Association Tool)
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This program calculates the multiple sequence alignment of k>1 DNA sequences.
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Scripts written to facilitate and analyze the functionalization of Cellulose nanocrystals and pABA ligands
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a robust FASTQ-specific compressor for recent generation data via score-based reordering
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Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram
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comparative population genomics and admixture analysis pipeline
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EnsemblToHGNCby vanallenlab
This script takes in a tab-separated file containing at least one column of Ensembl IDs and a string indicating the header for this column, and outputs a tab-separated file identical to the input file except that it has an additional column containing mapped HGNC gene symbols for each row.
Python 2Updated: 3 y ago License: No License (No License)
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interaction-viewerby ebi-uniprot
An adjacency graph visualisation of protein interaction data.
JavaScript 2Updated: 4 y ago License: Permissive (Apache-2.0)
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mustacheby durrantmm
A flexible tool to identify mobile genetic elements and their sites of insertions from short-read whole-genome sequencing data.
Python 2Updated: 5 y ago License: No License (No License)
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update_assemblyby phasegenomics
Generate two phased Juicebox .assembly files from one master .assembly for FALCON-Phase
Python 2Updated: 4 y ago License: Strong Copyleft (AGPL-3.0)
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immune-orthogonalby natepalmer
MHC binding analysis to define protein immune orthogonality. See Moreno et al. 2018.
Python 2Updated: 4 y ago License: No License (No License)
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MARVELby deyvidamgarten
MARVEL: Metagenomic Analyses and Retrieval of Viral Elements
Python 2Updated: 5 y ago License: Strong Copyleft (GPL-3.0)
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frXAS.pyby BGerwe
A package to process, analyze, and interpret data from frequency-resolved X-ray absorption spectroscopy measurements.
Python 2Updated: 3 y ago License: Proprietary (Proprietary)
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TADtreeby raphael-group
Python 2Updated: 4 y ago License: Permissive (BSD-3-Clause)
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ApeShapeby NCBI-Hackathons
A Prototype for Defining the Ancestral Alleles for Ones that Modify Human Phenotypes
Python 2Updated: 4 y ago License: Permissive (MIT)
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SCTCwhatateam-ShinyAppby pvvhoang
Python 2Updated: 4 y ago License: No License (No License)
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k
kmer-extract-by-trigger-siteby Comai-Lab
A script for extracting kmers (k base pair sized words) from fastq sequencing files after a specific trigger sequence.
Python 2Updated: 1 y ago License: Strong Copyleft (AGPL-3.0)
2Updated: 1 y ago License: Strong Copyleft (AGPL-3.0)Support
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MetaProgramsby nwheels-io
Provides static analysis, transformation, and code generation mechanisms in an extensible set of programming languages
C# 2Updated: 3 y ago License: Permissive (MIT)
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k
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protein_toolsby doubleQ2018
My own tools for protein structure
Python 2Updated: 4 y ago License: No License (No License)
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virKMERby jnoms
viral KMER enrichment - Used to enrich viral reads in an input dataset
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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SeniorProjectChromevolby DaniRuizPerez
BSc Senior Project, Bioinformatics Django web platform for storage and analysis of Biological data. Still in use by the group CHROMEVOL from FIU
Python 2Updated: 4 y ago License: Strong Copyleft (GPL-3.0)
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dna-alignment-jfarris587by IUDataStructuresCourse
dna-alignment-jfarris587 created by GitHub Classroom
Java 2Updated: 5 y ago License: No License (No License)
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EpiExplorerby aehrc
Python 2Updated: 4 y ago License: No License (No License)
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UMI-ATAC-seqby tzhu-bio
Python 2Updated: 3 y ago License: No License (No License)
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MultipleSequenceAlignmentby abishpius
Use this to search for any protein in the NCBI Database, align it to a reference sequence, and build a concensus sequence.
Python 2Updated: 4 y ago License: No License (No License)
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DoGFinderby yuvalwiesel
Recent studies discovered a widespread induction of transcriptional readthrough as a consequence of various stress conditions in mammalian cells. This novel phenomenon, initially identified from the analysis of RNA-seq data, suggests intriguing new levels of gene expression regulation. However, the mechanism underlying the readthrough phenomenon, as well as its regulatory consequences, still remain elusive. Furthermore, the readthrough response to stress has thus far not been investigated outside of mammalian species, and the occurrence of the readthrough phenomenon in many physiological and disease conditions remains to be explored. To facilitate a wider investigation into transcriptional readthrough, we created the DoGFinder software, which allows the identification and quantification of readthrough transcripts, DoGs, from any RNA-seq dataset. We further used DoGFinder to discover DoG induction in human PME cells following hypoxia – a previously unknown readthrough inducing stress type. This python based freely available software will enable users to explore, in a few simple steps, the readthrough phenomenon in any condition and organism.
Python 2Updated: 3 y ago License: No License (No License)
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StructuralMotifsby pdeford
Tools for finding and working with structural representations of DNA motifs.
Python 2Updated: 5 y ago License: Permissive (MIT)
2Updated: 5 y ago License: Permissive (MIT)Support
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vg_snakemakeby vgteam
Snakemake workflow for the vg toolkit.
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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organdietby maxibor
Metagenomics pipeline for human diet analysis using organelles genomes
Python 2Updated: 5 y ago License: Permissive (MIT)
2Updated: 5 y ago License: Permissive (MIT)Support
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Clustering-mRNA-Expression-Databy abishpius
Example of clustering mRNA expression data from the Cancer Cell Line Database.
Python 2Updated: 4 y ago License: No License (No License)
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selectable_pkg_variants_exampleby jjhelmus
Python 2Updated: 5 y ago License: No License (No License)
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cath_datasetsby wouterboomsma
Cath protein structure classification sets
Python 2Updated: 3 y ago License: Permissive (CC-BY-4.0)
2Updated: 3 y ago License: Permissive (CC-BY-4.0)Support
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gene-regulatory-networkby EliasPa
Assignment project 2. Identification of gene regulatory network from gene expression time-course data
Python 2Updated: 4 y ago License: No License (No License)
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falconby AustralianBioCommons
Python 2Updated: 3 y ago License: Permissive (Apache-2.0)
2Updated: 3 y ago License: Permissive (Apache-2.0)Support
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bcbio-utilsby bcbio
Helper scripts for bcbio-nextgen
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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gtracksby anthony-aylward
plot genome track data (for example from a BigWig file)
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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DependencyMapby timiles
Compare package dependencies across all your repositories
JavaScript 2Updated: 4 y ago License: Permissive (MIT)
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ContinuumRemovalby checongcong
Python 2Updated: 3 y ago License: No License (No License)
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dnacurveby cgohlke
DNA Curvature Analysis. Forked from https://pypi.org/project/dnacurve
Python 2Updated: 1 y ago License: Permissive (BSD-3-Clause)
2Updated: 1 y ago License: Permissive (BSD-3-Clause)Support
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ProtienSequencerby Ri2parna
Converting Codon Sequences to Corresponding Acid Sequences.
Python 2Updated: 3 y ago License: No License (No License)
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bulk-rnaseq-analysisby erilu
A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.
Python 2Updated: 4 y ago License: No License (No License)
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SAMPEIby FenyoLab
Python 2Updated: 3 y ago License: Permissive (MIT)
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traitar3by nick-youngblut
From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)
Python 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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strum_paperby pdeford
Supporting information for the paper "DNA shape complements sequence-based representations of transcription factor binding sites"
Python 2Updated: 5 y ago License: No License (No License)
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ramachandranby leovandriel
Make Ramachandran plots from pdb files
Python 2Updated: 4 y ago License: Permissive (MIT)
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NER-of-Experimental-Facilitiesby ljwmusclenlper
Python 2Updated: 4 y ago License: No License (No License)
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Gexploraby nthomasCUBE
Gexplora - user-interface to analyse genomic elements along chromosomes
Python 2Updated: 4 y ago License: No License (No License)
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GATby ch6845
GAT (Generic Genome-Wide Association Tool)
Python 2Updated: 3 y ago License: No License (No License)
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Multiple-sequence-alignmentby EranCohenSW
This program calculates the multiple sequence alignment of k>1 DNA sequences.
Java 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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functionalizedCelluloseby jordancaraballo
Scripts written to facilitate and analyze the functionalization of Cellulose nanocrystals and pABA ligands
Python 2Updated: 3 y ago License: No License (No License)
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FastqCLSby Krlucete
a robust FASTQ-specific compressor for recent generation data via score-based reordering
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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locus2genoplotrby metagenlab
Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram
Python 2Updated: 3 y ago License: No License (No License)
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cpgapby LabBandSB
comparative population genomics and admixture analysis pipeline
Python 2Updated: 4 y ago License: No License (No License)
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GeneAlloyby Edinburgh-Genome-Foundry
Python 2Updated: 3 y ago License: Permissive (MIT)
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