olgabot

latex-moderncv

My latex resume using the moderncv template

dotfiles

Collection of rc files for easy portability

bonvoyage

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

clippy-kindle

Create flashcards and markdown files from your Kindle notes/highlights.

lsd

The next gen ls command

orpheum

Orpheum is a Python package for directly predicting open reading frames (ORFs) by translating RNA-seq reads into coding protein sequence.

psytoolkit-analysis

Analyze psytoolkit data

rnaseq-nf

A proof of concept of RNAseq pipeline

10xdash

Pairwise similarity metrics for 10x barcoded RNASeq datasets

2021-paper-metapangenomes

2022-ced9-bcl2

Structural homology between C. elegans Ced9 and human BCL2

2022-mouse-lemur-tabula-microcebus

Code for cross-species and uTAR sequence homology analyses for two Tabula Microcebus papers

2022-sourmash-multigather-kmer-stats

Do sourmash multigather, but use a background k-mer distribution model to quantify significance of matches, and report all matching k-mer sequences

2022-sourmash-multisearch

Search multiple query k-mer signatures against a database

2023-functional-homology-paper

botryllus-mhc

Code for early marine cordate, Botryllus schlosseri, and human-mouse MHC homology paper

nf-core-funcanno

Nextflow pipeline for functional annotation of protein sequences, focused on emerging model organisms without reference genomes

nf-core-kmerseek

nf-core-sourcecred

Nextflow sourcecred

nf-functionalhomology

Identifies protein sequence pairs with functional homology, but may not have sequence homology

olgabotvinnik.com

Personal website

paperpile-notion

One-way sync Paperpile with Notion

pyo3_branchwater

Python plugin for fast search & gather

qvalue

R package to estimate q-values and false discovery rate quantities.

scrnaseq-for-the-99-percent

Code accompanying the paper titled, "Single-cell transcriptomics for the 99.9% of species without reference genomes" by Botvinnik et al, 2021

SPLASH

swan_vis

A Python library to visualize and analyze long-read transcriptomes

sync-paperpile-notion-v2

Sync paperpile to notion

sync-paperpile-to-notion

Sync paperpile library to notion

testpipeline

A small example pipeline used to test new nf-core infrastructure and common code.