Olga Botvinnik

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 lab

latex-moderncv. My latex resume using the moderncv template

cshl-singlecell-2017. Single Cell Analysis course at Cold Spring Harbor Laboratory 2017

sciencemeetproductivity.tumblr.com. backup of old blog at sciencemeetproductivity.tumblr.com

abi2fastq. abi2fastq is a small utility to convert Sanger sequencing reads in .abi (applied biosystems) format to FASTQ

kvector. kvector is a small utility for converting motifs to kmer vectors to compare motifs of different lengths

cheatsheets. Quick lookup documents for commonly used tools

sj2psi. Convert RNA-STAR aligner "SJ.out.tab" files to "Percent spliced-in" (Psi) scores

twerk. 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 Biology

seaborn. Improved matplotlib for statistical data visualization

poshsplice. PoshSplice is a collection of scripts and functions used to annotate splicing events, exons, and their functional consequences

dotfiles. Collection of rc files for easy portability

macosko2015. Expression data for Macosko et al, "Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets," Cell (2015)

codeneuro_sf2015_dataset_packaging. Notes from dataset packaging subgroup at CodeNeuro

etframes. Edward Tufte's ideas, applied to matplotlib

wasabiplot. WasabiPlot is a flexible coverage and junction read plotter that heavily borrows from MISO's SashimiPlot

bonvoyage. Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.

cupcake. :coffee: :cake: Bite-sized machine learning visualizations

pyhomer. Utility functions to work with output from the HOMER motif finding program

permission-letters. LaTeX template for creating co-author permission letters for UCSD dissertation submissions

olgabot.github.io-source-deprecated. Source code for blog, autodeployed using Travis-CI

gscripts. General Use Scripts and Helper functions

lsd. The next gen ls command

cookiecutter-pypackage. Cookiecutter template for a Python package. See https://github.com/audreyr/cookiecutter.

nextflow-each-metadata-error. Repo to test nextflow `each` directive with metadata