Ryan Dale (@daler)
github

daler

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  • Stars
    star
    981
  • Global Rank 31,252 (Top 2 %)
  • Followers 318
  • Following 28
  • Registered over 15 years ago
  • Most used languages
    Python
         84.8 %
    JavaScript
         6.1 %
    HTML
         3.0 %
    R
         3.0 %
    Shell
         3.0 %
  • Location 🇺🇸 United States
  • Country Total Rank 9,522
  • Country Ranking
    Python
         1,574
    R
         5,024
    Shell
         5,617

Top repositories

1

pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
Python
297
star
2

gffutils

GFF and GTF file manipulation and interconversion
Python
284
star
3

metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data
Python
87
star
4

trackhub

create, manage, and upload track hubs for use in the UCSC genome browser
Python
51
star
5

matplotlibrc

some example matplotlibrc files, and a script display their effects
Python
48
star
6

sphinxdoc-test

experimenting with the best way to push sphinx-generated docs to gh-pages
24
star
7

dotfiles

dotfiles, batteries included
Shell
18
star
8

hubward

Manage the visualization of large amounts of other people's [often messy] genomics data
Python
18
star
9

pipeline-example

example ruffus pipeline
Python
18
star
10

biomartpy

Simple interface to BioMart (Python -> rpy2 -> R/BioConductor's biomaRt)
Python
17
star
11

chromhmm-tools

Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)
Python
16
star
12

ucscsession

Python package for managing sessions in the UCSC Genome Browser.
Python
11
star
13

blender-for-3d-printing

Material for introductory course on using Blender for 3D printing
Python
11
star
14

rdbio-scripts

Unorganized collection of bioinformatics scripts and utilities
Python
10
star
15

GFFutils_old

NOTE: see new version at https://github.com/daler/gffutils.
Python
10
star
16

encode-dataframe

Convert UCSC's ENCODE metadata into pandas DataFrames
Python
9
star
17

enhancer-snakemake-demo

Demos a Snakemake workflow to classify enhancer regions based on publicly available chromatin marks.
Python
6
star
18

genomicfeatures

Python
5
star
19

gdc

Genomic Dataset Constructor: create example BED, GFF, SAM, FASTQ files from "ASCII art" definitions
Python
5
star
20

ontologization

Wrapper for Ontologizer gene ontology analysis tool, with manipulation and display of downstream results
Python
5
star
21

seqprint

pretty-print genomic sequences
Python
4
star
22

metaseq-biotrac56

Materials for the metaseq presentation at NIH FAES Bio-Trac 56 (http://www.biotrac.com/pages/Tracs/Trac56.html)
Python
4
star
23

deseq-browser

View DESeq results in a web browser, with filtering and searching
JavaScript
3
star
24

shiny-fet

Shiny app for visualizing the results of a Fisher's exact test
R
3
star
25

metaseq-example-data

Example data for metaseq
Python
2
star
26

chromhmm-enhancers-umel

Identify enhancers. Includes data download, liftover, parallelized workflows, results aggregation, and example output.
Python
2
star
27

sphinxleash

Lightweight framework for programatically generating Sphinx docs.
Python
2
star
28

docker-rw2019

Materials for docker demonstration for Spring 2019 Reproducibility Workshop
HTML
2
star
29

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
Python
2
star
30

entabled

Convert text data files to a browser-viewable version that can be searched, filtered, and sorted
JavaScript
2
star
31

marginalhists

Scatterplots with marginal histograms using matplotlib
Python
1
star
32

trackhub-demo

Python
1
star
33

build-test

sandbox for bioconda-utils
Python
1
star
34

hubward-studies

Config files for running hubward on published data sets.
Python
1
star