Olga Botvinnik

Login: olgabot

Company: @czbiohub

Location: San Francisco, CA

Bio: peppy computational biologist

Blog: www.olgabotvinnik.com

Blog: www.olgabotvinnik.com

Member of

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Repositories

abi2fastq

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

algorithm-template

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anchor

Anchor: Find bimodal, unimodal, and multimodal features in your data

awesome

:sunglasses: Curated list of awesome lists

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bedtools_flank_seq_strand_test

Repository to test bedtools flank/fasta/strand confusion

bioconda-recipes

Conda recipes for the bioconda channel.

bioconda-utils

Utilities for building and managing bioconda recipes

biogo

biogo is a bioinformatics library for Go

biom262-2016

Code and notebooks for BIOM262

bionode-gsnap

Node.js interface to the GSNAP spliced aligner for RNA-Seq

bionode-ncbi

Node.js module for working with the NCBI API (aka e-utils).

bionode-star

Node.js interface to the STAR spliced aligner for RNA-Seq

biopython

Official git repository for Biopython (converted from CVS)

bonvoyage

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

cheatsheets

Quick lookup documents for commonly used tools

circle-time

Circular graphic representation of time spent during the day

clustering_on_transcript_compatibility_counts

Clustering cells from single cell RNA seq assays

codeneuro_sf2015_dataset_packaging

Notes from dataset packaging subgroup at CodeNeuro

coding-cucumber

Code used in the blog: blog.olgabotvinnik.com. Name origin: I code and I like cucumbers.

combat.py

python / numpy / pandas / patsy version of ComBat for removing batch effects.

cookiecutter-pypackage

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

cshl-singlecell-2017

Single Cell Analysis course at Cold Spring Harbor Laboratory 2017

cupcake

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

czbiohub

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dalliance

Interactive web-based genome browser.

dash

Interactive, reactive web apps in pure python :level_slider: :bar_chart:

Deedy-Resume

A one page , two asymmetric column resume template in XeTeX that caters to an undergraduate Computer Science student

deep_learning_papers

A place to collect papers that are related to deep learning and computational biology

deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

dionysus

Library for computing persistent homology

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

dnasequenceassembler

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dupe

Get "dupes" of expensive skincare and haircare products with machine learning on the ingredient list

dynamicTreeCut

Python translation of the hybrid dynamicTreeCut method as created by Peter Langfelder and Bin Zhang.

easy-data

easy access to benchmark datasets

etframes

Edward Tufte's ideas, applied to matplotlib

free-programming-books

:books: Freely available programming books

gatk

GATK Official Release Repository

gbic-ucsd.github.io-source

Source code for building the static website gbic-ucsd.github.io using Pelican (Python framework)

generators

Generators for Stream Data Processing, or Generator Showcase Showdown

gffutils

GFF and GTF file manipulation and interconversion

gitignore

A collection of useful .gitignore templates

goatools

Python scripts to find enrichment of GO terms

GPfates

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gscripts

General Use Scripts and Helper functions

GSEApy

Gene Set Enrichment Analysis in Python

hugo-sustain

? Personal blog theme built with Bootstrap, powered by Hugo.

ig_repertoire_constructor

An algorithm for error-correction of immunosequencing Illumina MiSeq reads and immunoproteogenomic analysis

illumina

bíogo illumina utilities repository

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

ipython_d3_mashup

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ipython_nb_cluster

Scripts to launch IPython parallel on a cluster and run an IPython Notebook to run the analysis.

javascript-koans

Koans to learn Javascript

jlSimplex

Proof-of-concept implementation of the (dual) simplex algorithm for linear programming in Julia.

joypy

Joyplots in matplotlib + pandas

jupyter-themer

Apply custom CSS styling to your jupyter notebooks

Keras-genomics

Perform hyper-parameter tuning, training, testing and prediction with Keras

knowledge-repo

A next-generation curated knowledge sharing platform for data scientists and other technical professions.

kvector

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

latex-moderncv

My latex resume using the moderncv template

libglvnd

The GL Vendor-Neutral Dispatch library

lonnberg_svensson2017

Expression data for Lönnberg + Svensson et al, "Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria," Science Immunology (2017)

macosko2015

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

magic

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matplotlib

matplotlib: plotting with Python

matplotlib-venn

Area-weighted venn-diagrams for Python/matplotlib

mcorbit

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metaseq

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

MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

mit-license

Hosted MIT License with details controlled through this repo

mpld3

D3 Renderings of Matplotlib Graphics

olgabot.github.io-deprecated

Portfolio

olgabot.github.io-source-deprecated

Source code for blog, autodeployed using Travis-CI

olgabotvinnik.com

Personal website

olgabotvinnik.com-hugo-fail

Failed attempt at getting hugo and themes to work

open-women

List of women in open source, open science, open access fields

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

pelican-plugins

Collection of plugins for the Pelican static site generator

people

Pelican extension to auto-generate a people page given their markdown files

permission-letters

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

peterdowns.com

My personal website

PhenoGraph

Subpopulation detection in high-dimensional single-cell data

pim

:handbag: friendly command-line tool for initializing python packages

polo

Python Optimal Leaf Ordering for Hierarchical Clustering

poshsplice

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

prettyplotlib

Painlessly create beautiful matplotlib plots.

pullkee

A simple Pull Requests analyzer

pure-single

Single blogging theme for Pelican blogs

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

PyCharm-Python-Templates

Python Templates for the PyCharm IDE

pycon2014_dataviz

Computational data visualization. Presented at PyCon 2014 lightning talks.

pydata2014biobof

PyData NYC 2014 Biological Data Science Birds of a Feather

pydata2014biodata

Slides and ipython notebooks accompanying talk given at PyData NYC 2014

pyhomer

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

python-pds

Toy Implementation of Probabilistic Data Structures in Python (PyData 2013)

qtools

qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python

rcfiles

Collection of rc files for easy portability

reflow

A language and runtime for distributed, incremental data processing in the cloud

resume

My resume as a PDF including the well commented LaTeX source and build instructions.

rnaseek

Scripts and modules for parsing and aggregating output files from RNA-sequencing data

rnaseq

bíogo RNAseq utilities repository

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).

robust-pca

A simple Python implementation of R-PCA

roi-model

Specification for a common ROI model

salk_comp_jc_monocle

Tutorial for Salk Journal club on the Monocle package

sciencemeetproductivity.tumblr.com

backup of old blog at sciencemeetproductivity.tumblr.com

scihub-manuscript

Manuscript for the Sci-Hub Coverage Study

scikit-learn

scikit-learn: machine learning in Python

scipy

Scipy library main repository

seaborn

Improved matplotlib for statistical data visualization

seaborn_factorplot_pointplot_valueerror

Repo demonstrating error with seaborn factorplot with pointplot (but not barplot)

segerstolpe_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)

shields

Shields badge specification, website and default API server

sj2psi

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

sleuth

Inspect kallisto RNA-Seq output

sourmash

Compute and compare MinHash signatures for DNA data sets.

sphinx-deployment

automatic setup and deployment for sphinx docs

spliceworld

The Whys and Hows of annotating alternative splicing events

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

starfish

*fish -- a standardized analysis pipeline for image-based transcriptomics

statsmodels

Statsmodels: statistical modeling and econometrics in Python

swc-davis-t3-bio

2015 Davis software carpentry train-the-trainers (t3) day 3 with bio only

tabula-muris

Code and annotations for the Tabula Muris single-cell transcriptomic dataset.

tensorboard

TensorFlow's Visualization Toolkit

test

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treecut

Find nodes in hierarchical clustering that are statistically significant

twenty-pelican-html5up

This is an adaptation of the html5up template "Twenty" for the Python static site generator Pelican.

twerk

Network analysis of correlations (WGCNA-inspired)

ucsd-thesis

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velocyto.py

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vim-pizza

My initial attempt at trying to order pizza from within vim.

wasabiplot

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

wLib

Python Modules for High-throughput Sequencing Data Analysis

workshop-template

Template for workshop websites.

Commits To