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prettyplotlib
Painlessly create beautiful matplotlib plots.rna-seq-diff-exprn
RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).awesome-expectations
Examples of great academic lab expectations, manuals, policies for joining and being in the labcshl-singlecell-2017
Single Cell Analysis course at Cold Spring Harbor Laboratory 2017sciencemeetproductivity.tumblr.com
backup of old blog at sciencemeetproductivity.tumblr.comcheatsheets
Quick lookup documents for commonly used toolsabi2fastq
abi2fastq is a small utility to convert Sanger sequencing reads in .abi (applied biosystems) format to FASTQsj2psi
Convert RNA-STAR aligner "SJ.out.tab" files to "Percent spliced-in" (Psi) scoreskvector
kvector is a small utility for converting motifs to kmer vectors to compare motifs of different lengthstwerk
Network analysis of correlations (WGCNA-inspired)dissertation
Computational analysis of single-cell alternative splicing: A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biologydotfiles
Collection of rc files for easy portabilitycodeneuro_sf2015_dataset_packaging
Notes from dataset packaging subgroup at CodeNeuroposhsplice
PoshSplice is a collection of scripts and functions used to annotate splicing events, exons, and their functional consequencesmacosko2015
Expression data for Macosko et al, "Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets," Cell (2015)gscripts
General Use Scripts and Helper functionsbonvoyage
Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.olgabot.github.io-source-deprecated
Source code for blog, autodeployed using Travis-CIpermission-letters
LaTeX template for creating co-author permission letters for UCSD dissertation submissionssegerstolpe_palasantza2016
Expression and metadata for Segerstolpe + Palasantza et al, "Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes" in Cell Metabolism (2016)open-women
List of women in open source, open science, open access fieldspycon2014_dataviz
Computational data visualization. Presented at PyCon 2014 lightning talks.circle-time
Circular graphic representation of time spent during the daypsytoolkit-analysis
Analyze psytoolkit datapydata2014biodata
Slides and ipython notebooks accompanying talk given at PyData NYC 2014pyhomer
Utility functions to work with output from the HOMER motif finding programrnaseek
Scripts and modules for parsing and aggregating output files from RNA-sequencing datanextflow-each-metadata-error
Repo to test nextflow `each` directive with metadataLove Open Source and this site? Check out how you can help us