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pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")gffutils
GFF and GTF file manipulation and interconversionmetaseq
Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq datatrackhub
create, manage, and upload track hubs for use in the UCSC genome browsermatplotlibrc
some example matplotlibrc files, and a script display their effectssphinxdoc-test
experimenting with the best way to push sphinx-generated docs to gh-pagesdotfiles
dotfiles, batteries includedhubward
Manage the visualization of large amounts of other people's [often messy] genomics datapipeline-example
example ruffus pipelinebiomartpy
Simple interface to BioMart (Python -> rpy2 -> R/BioConductor's biomaRt)chromhmm-tools
Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)ucscsession
Python package for managing sessions in the UCSC Genome Browser.blender-for-3d-printing
Material for introductory course on using Blender for 3D printingrdbio-scripts
Unorganized collection of bioinformatics scripts and utilitiesGFFutils_old
NOTE: see new version at https://github.com/daler/gffutils.encode-dataframe
Convert UCSC's ENCODE metadata into pandas DataFramesenhancer-snakemake-demo
Demos a Snakemake workflow to classify enhancer regions based on publicly available chromatin marks.genomicfeatures
gdc
Genomic Dataset Constructor: create example BED, GFF, SAM, FASTQ files from "ASCII art" definitionsontologization
Wrapper for Ontologizer gene ontology analysis tool, with manipulation and display of downstream resultsseqprint
pretty-print genomic sequencesmetaseq-biotrac56
Materials for the metaseq presentation at NIH FAES Bio-Trac 56 (http://www.biotrac.com/pages/Tracs/Trac56.html)deseq-browser
View DESeq results in a web browser, with filtering and searchingshiny-fet
Shiny app for visualizing the results of a Fisher's exact testmetaseq-example-data
Example data for metaseqchromhmm-enhancers-umel
Identify enhancers. Includes data download, liftover, parallelized workflows, results aggregation, and example output.docker-rw2019
Materials for docker demonstration for Spring 2019 Reproducibility Workshopfeature-by-reads-matrix
Collection of scripts to create a table of genome features with the number of reads per feature for an arbitrary number of samplesentabled
Convert text data files to a browser-viewable version that can be searched, filtered, and sortedmarginalhists
Scatterplots with marginal histograms using matplotlibtrackhub-demo
build-test
sandbox for bioconda-utilshubward-studies
Config files for running hubward on published data sets.Love Open Source and this site? Check out how you can help us