Pinned Repositories
orpheum
Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein sequence.
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
seaborn
Statistical data visualization in Python
kmermaid
k-mer similarity analysis pipeline
awesome-expectations
Examples of great academic lab expectations, manuals, policies for joining and being in the lab
cshl-singlecell-2017
Single Cell Analysis course at Cold Spring Harbor Laboratory 2017
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
latex-moderncv
My latex resume using the moderncv template
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).
olgabot's Repositories
olgabot/latex-moderncv
My latex resume using the moderncv template
olgabot/dotfiles
Collection of rc files for easy portability
olgabot/bonvoyage
Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.
olgabot/lsd
The next gen ls command
olgabot/nextflow-each-metadata-error
Repo to test nextflow `each` directive with metadata
olgabot/orpheum
Orpheum is a Python package for directly predicting open reading frames (ORFs) by translating RNA-seq reads into coding protein sequence.
olgabot/psytoolkit-analysis
Analyze psytoolkit data
olgabot/rnaseq-nf
A proof of concept of RNAseq pipeline
olgabot/10xdash
Pairwise similarity metrics for 10x barcoded RNASeq datasets
olgabot/2021-paper-metapangenomes
olgabot/2022-ced9-bcl2
Structural homology between C. elegans Ced9 and human BCL2
olgabot/2022-mouse-lemur-tabula-microcebus
Code for cross-species and uTAR sequence homology analyses for two Tabula Microcebus papers
olgabot/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
olgabot/2022-sourmash-multisearch
Search multiple query k-mer signatures against a database
olgabot/2023-functional-homology-paper
olgabot/botryllus-mhc
Code for early marine cordate, Botryllus schlosseri, and human-mouse MHC homology paper
olgabot/nf-core-funcanno
Nextflow pipeline for functional annotation of protein sequences, focused on emerging model organisms without reference genomes
olgabot/nf-core-kmerseek
olgabot/nf-core-sourcecred
Nextflow sourcecred
olgabot/nf-functionalhomology
Identifies protein sequence pairs with functional homology, but may not have sequence homology
olgabot/olgabotvinnik.com
Personal website
olgabot/paperpile-notion
One-way sync Paperpile with Notion
olgabot/pyo3_branchwater
Python plugin for fast search & gather
olgabot/qvalue
R package to estimate q-values and false discovery rate quantities.
olgabot/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
olgabot/SPLASH
olgabot/swan_vis
A Python library to visualize and analyze long-read transcriptomes
olgabot/sync-paperpile-notion-v2
Sync paperpile to notion
olgabot/sync-paperpile-to-notion
Sync paperpile library to notion
olgabot/testpipeline
A small example pipeline used to test new nf-core infrastructure and common code.