daler

matplotlibrc

some example matplotlibrc files, and a script display their effects

pipeline-example

example ruffus pipeline

biomartpy

Simple interface to BioMart (Python -> rpy2 -> R/BioConductor's biomaRt)

ucscsession

Python package for managing sessions in the UCSC Genome Browser.

GFFutils_old

NOTE: see new version at https://github.com/daler/gffutils.

encode-dataframe

Convert UCSC's ENCODE metadata into pandas DataFrames

enhancer-snakemake-demo

Demos a Snakemake workflow to classify enhancer regions based on publicly available chromatin marks.

gdc

Genomic Dataset Constructor: create example BED, GFF, SAM, FASTQ files from "ASCII art" definitions

genomicfeatures

ontologization

Wrapper for Ontologizer gene ontology analysis tool, with manipulation and display of downstream results

metaseq-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 searching

seqprint

pretty-print genomic sequences

entabled

Convert text data files to a browser-viewable version that can be searched, filtered, and sorted

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

metaseq-example-data

Example data for metaseq

bedtools

A flexible suite of utilities for genome arithmetic. That is, set theory on genomic features.

marginalhists

Scatterplots with marginal histograms using matplotlib

bedtools2

A powerful toolset for genome arithmetic.

figshare

Command line client for figshare

linregress

Small package for managing linear regression in R from Python via rpy2

matplotlib

matplotlib: plotting with Python

pytrackhub

Python module that will allow users to generate trackhub's for UCSC Genome Browser

scurgen

A tool for exploring genomic data with space filling curves

SimpleSnakemakeTutorial