daler/pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

Language: Python - Size: 28.2 MB - Last synced: 2 days ago - Pushed: 9 days ago - Stars: 293 - Forks: 104

daler/dotfiles

dotfiles, batteries included

Language: Shell - Size: 3.17 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 15 - Forks: 11

daler/vim-python-pep8-indent Fork of Vimjas/vim-python-pep8-indent

A nicer Python indentation style for vim.

Language: Vim Script - Size: 156 KB - Last synced: 8 days ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

daler/vogt-particle-tracking

Code to reproduce analysis from Vogt et al 2019 Nature Communications

Language: Jupyter Notebook - Size: 5.32 MB - Last synced: 8 days ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

daler/rsconnect Fork of rstudio/rsconnect

Publish Shiny Applications, RMarkdown Documents, Jupyter Notebooks, Plumber APIs, and more

Language: R - Size: 7.93 MB - Last synced: 8 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

daler/sphinxleash

Lightweight framework for programatically generating Sphinx docs.

Language: Python - Size: 273 KB - Last synced: 8 days ago - Pushed: over 8 years ago - Stars: 2 - Forks: 1

daler/seqprint

pretty-print genomic sequences

Language: Python - Size: 211 KB - Last synced: 8 days ago - Pushed: over 9 years ago - Stars: 3 - Forks: 0

daler/shiny-fet

Shiny app for visualizing the results of a Fisher's exact test

Language: R - Size: 2.93 KB - Last synced: 8 days ago - Pushed: over 7 years ago - Stars: 3 - Forks: 0

daler/scurgen Fork of arq5x/scurgen

A tool for exploring genomic data with space filling curves

Language: Python - Size: 3.78 MB - Last synced: 8 days ago - Pushed: about 11 years ago - Stars: 0 - Forks: 1

daler/rdbio-scripts

Unorganized collection of bioinformatics scripts and utilities

Language: Python - Size: 279 KB - Last synced: 8 days ago - Pushed: over 7 years ago - Stars: 10 - Forks: 6

daler/pytrackhub Fork of vsmalladi/pytrackhub

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

Language: Python - Size: 75.2 KB - Last synced: 8 days ago - Pushed: over 11 years ago - Stars: 0 - Forks: 0

daler/NIHCloudLabAWS Fork of STRIDES/NIHCloudLabAWS

Documentation and tutorials on using AWS for biomedical research

Language: Jupyter Notebook - Size: 44.6 MB - Last synced: 8 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

daler/metaseq-example-data

Example data for metaseq

Language: Python - Size: 89.6 MB - Last synced: 8 days ago - Pushed: about 9 years ago - Stars: 2 - Forks: 1

daler/ontologization

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

Language: Python - Size: 141 KB - Last synced: 8 days ago - Pushed: about 11 years ago - Stars: 5 - Forks: 2

daler/metaseq-biotrac56

Materials for the metaseq presentation at NIH FAES Bio-Trac 56 (http://www.biotrac.com/pages/Tracs/Trac56.html)

Language: Python - Size: 5.48 MB - Last synced: 8 days ago - Pushed: about 9 years ago - Stars: 4 - Forks: 0

daler/hubward-studies

Config files for running hubward on published data sets.

Language: Python - Size: 715 KB - Last synced: 8 days ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0

daler/GFFutils_old

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

Language: Python - Size: 683 KB - Last synced: 8 days ago - Pushed: over 13 years ago - Stars: 10 - Forks: 7

daler/marginalhists

Scatterplots with marginal histograms using matplotlib

Language: Python - Size: 188 KB - Last synced: 8 days ago - Pushed: over 11 years ago - Stars: 1 - Forks: 0

daler/linregress

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

Language: Python - Size: 89.8 KB - Last synced: 8 days ago - Pushed: over 11 years ago - Stars: 0 - Forks: 0

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

Language: Python - Size: 105 KB - Last synced: 8 days ago - Pushed: over 13 years ago - Stars: 2 - Forks: 0

daler/erythroid-genes

Documents the construction of mouse erythroid gene lists

Language: HTML - Size: 198 KB - Last synced: 8 days ago - Pushed: about 7 years ago - Stars: 0 - Forks: 1

daler/enhancer-snakemake-demo

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

Language: Python - Size: 4.43 MB - Last synced: 8 days ago - Pushed: over 9 years ago - Stars: 6 - Forks: 2

daler/bioconda-utils Fork of bioconda/bioconda-utils

Utilities for building and managing bioconda recipes

Language: Python - Size: 5.89 MB - Last synced: 8 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

daler/entabled

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

Language: JavaScript - Size: 922 KB - Last synced: 8 days ago - Pushed: about 11 years ago - Stars: 2 - Forks: 0

daler/encode-dataframe

Convert UCSC's ENCODE metadata into pandas DataFrames

Language: Python - Size: 418 KB - Last synced: 8 days ago - Pushed: over 9 years ago - Stars: 9 - Forks: 0

daler/docker-dokuwiki Fork of linuxserver/docker-dokuwiki

Size: 200 KB - Last synced: 8 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

daler/docker-rw2019

Materials for docker demonstration for Spring 2019 Reproducibility Workshop

Language: HTML - Size: 89.8 KB - Last synced: 8 days ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 0

daler/connect-test

temp repo for testing github status updates

Size: 0 Bytes - Last synced: 8 days ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

daler/deseq-browser

View DESeq results in a web browser, with filtering and searching

Language: JavaScript - Size: 918 KB - Last synced: 8 days ago - Pushed: about 11 years ago - Stars: 3 - Forks: 0

daler/build-test

sandbox for bioconda-utils

Language: Python - Size: 25.4 KB - Last synced: 8 days ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0

daler/chromhmm-enhancers-umel

Identify enhancers. Includes data download, liftover, parallelized workflows, results aggregation, and example output.

Language: Python - Size: 1020 KB - Last synced: 8 days ago - Pushed: about 7 years ago - Stars: 2 - Forks: 1

daler/bioconda-recipes Fork of bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

Language: Shell - Size: 147 MB - Last synced: 8 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

daler/biomartpy

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

Language: Python - Size: 146 KB - Last synced: 8 days ago - Pushed: almost 10 years ago - Stars: 16 - Forks: 3

daler/aerial.nvim Fork of stevearc/aerial.nvim

Neovim plugin for a code outline window

Size: 812 KB - Last synced: 8 days ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

daler/gffutils

GFF and GTF file manipulation and interconversion

Language: Python - Size: 30.9 MB - Last synced: 8 days ago - Pushed: 23 days ago - Stars: 267 - Forks: 74

daler/trackhub

create, manage, and upload track hubs for use in the UCSC genome browser

Language: Python - Size: 13.3 MB - Last synced: 8 days ago - Pushed: 16 days ago - Stars: 51 - Forks: 20

daler/trackhub-demo

Language: Python - Size: 596 KB - Last synced: 8 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 0

daler/metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data

Language: Python - Size: 23.7 MB - Last synced: 8 days ago - Pushed: over 3 years ago - Stars: 87 - Forks: 36

daler/sphinxdoc-test

experimenting with the best way to push sphinx-generated docs to gh-pages

Size: 502 KB - Last synced: 8 days ago - Pushed: almost 9 years ago - Stars: 24 - Forks: 31

daler/blender-for-3d-printing

Material for introductory course on using Blender for 3D printing

Language: Python - Size: 3.47 MB - Last synced: 8 days ago - Pushed: almost 8 years ago - Stars: 10 - Forks: 2

daler/zenburn.nvim Fork of phha/zenburn.nvim

Zenburn for the modern age

Language: Lua - Size: 1.39 MB - Last synced: 8 days ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

daler/matplotlibrc

some example matplotlibrc files, and a script display their effects

Language: Python - Size: 3.85 MB - Last synced: 8 days ago - Pushed: over 10 years ago - Stars: 49 - Forks: 12

daler/hubward

Manage the visualization of large amounts of other people's [often messy] genomics data

Language: Python - Size: 1000 KB - Last synced: 7 days ago - Pushed: about 8 years ago - Stars: 18 - Forks: 4

daler/ucscsession

Python package for managing sessions in the UCSC Genome Browser.

Language: Python - Size: 173 KB - Last synced: 8 days ago - Pushed: about 9 years ago - Stars: 11 - Forks: 1

daler/chromhmm-tools

Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)

Language: Python - Size: 4.88 KB - Last synced: 8 days ago - Pushed: about 6 years ago - Stars: 15 - Forks: 2

daler/gdc

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

Language: Python - Size: 6.24 MB - Last synced: 8 days ago - Pushed: almost 13 years ago - Stars: 5 - Forks: 1

daler/genomicfeatures

Language: Python - Size: 51.1 MB - Last synced: 8 days ago - Pushed: about 13 years ago - Stars: 5 - Forks: 0

daler/pipeline-example

example ruffus pipeline

Language: Python - Size: 121 KB - Last synced: 8 days ago - Pushed: over 12 years ago - Stars: 18 - Forks: 3

daler/Pharmacogenomics_Prediction_Pipeline_P3 Fork of NCBI-Hackathons/Pharmacogenomics_Prediction_Pipeline_P3

Language: R - Size: 62 MB - Last synced: 8 days ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

daler/2015-09-09-NIH

Language: Python - Size: 910 KB - Last synced: 8 days ago - Pushed: over 8 years ago - Stars: 0 - Forks: 7

daler/bedtools2 Fork of arq5x/bedtools2

A powerful toolset for genome arithmetic.

Language: C++ - Size: 23.3 MB - Last synced: 8 days ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0

daler/figshare Fork of rmcgibbo/figshare

Command line client for figshare

Language: Python - Size: 160 KB - Last synced: 8 days ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0

daler/SimpleSnakemakeTutorial Fork of seandavi/SimpleSnakemakeTutorial

Language: Shell - Size: 40.4 MB - Last synced: 8 days ago - Pushed: about 10 years ago - Stars: 0 - Forks: 0

daler/bedtools Fork of arq5x/bedtools

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

Language: C++ - Size: 455 MB - Last synced: 8 days ago - Pushed: over 10 years ago - Stars: 1 - Forks: 0

daler/matplotlib Fork of matplotlib/matplotlib

matplotlib: plotting with Python

Language: Python - Size: 129 MB - Last synced: 8 days ago - Pushed: over 11 years ago - Stars: 0 - Forks: 0