daler/enhancer-snakemake-demo
Demos a Snakemake workflow to classify enhancer regions based on publicly available chromatin marks.
Developer Profile
daler
Discovered public repositories for daler in the GitHub catalog.
daler/chromhmm-tools
Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)
daler/matplotlibrc
some example matplotlibrc files, and a script display their effects
daler/ontologization
Wrapper for Ontologizer gene ontology analysis tool, with manipulation and display of downstream results
daler/entabled
Convert text data files to a browser-viewable version that can be searched, filtered, and sorted
daler/deseq-browser
View DESeq results in a web browser, with filtering and searching
daler/biomartpy
Simple interface to BioMart (Python -> rpy2 -> R/BioConductor's biomaRt)
daler/ucscsession
Python package for managing sessions in the UCSC Genome Browser.
daler/trackhub
create, manage, and upload track hubs for use in the UCSC genome browser
daler/scurgen
A tool for exploring genomic data with space filling curves
daler/marginalhists
Scatterplots with marginal histograms using matplotlib
daler/linregress
Small package for managing linear regression in R from Python via rpy2
daler/seqprint
pretty-print genomic sequences
daler/metaseq
Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data
daler/gffutils
GFF and GTF file manipulation and interconversion
daler/pipeline-example
example ruffus pipeline
daler/gdc
Genomic Dataset Constructor: create example BED, GFF, SAM, FASTQ files from "ASCII art" definitions
daler/genomicfeatures
Public repository.
daler/sphinxdoc-test
experimenting with the best way to push sphinx-generated docs to gh-pages
daler/rdbio-scripts
Unorganized collection of bioinformatics scripts and utilities
daler/pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
daler/GFFutils_old
NOTE: see new version at https://github.com/daler/gffutils.
daler/feature-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 samples