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allenbrainatlas

biogps

Gene expression measurements across various tissues using the BioGPS database

blast

Find homologs and ident values from an inputted list of genes

calcium_imaging

Tools to process calcium imaging data, including exporting images to videos, and analyzing videos via Suite2P

cavestory-development

All of the source code from my Remaking Cavestory in C++ youtube series can be found in this repository.

ctd

Query the Comparative Toxicogenomics Database for gene, chemical, and disease associations

datasharing

The Leek group guide to data sharing

david

For use with data from the functional annotation analysis tool DAVID

deepchem

Deep-learning models for Drug Discovery and Quantum Chemistry

docker-python

Kaggle Python docker image

fai-notes

Some notes, tutorials, and some experimentation with the fast.ai library (https://github.com/fastai/fastai)

galaxy_blast

Galaxy wrappers for NCBI BLAST+ and related BLAST tools.

genenetwork

Find common genes, phenotypes, and SNP locations from the phenogenomics database GeneNetwork

genlasso

Path algorithm for generalized lasso problems

geo

Tools for the Gene Expression Omnibus

megena

Multiscale embedded gene co-expression network analysis

mgi

Find mouse-human homologs using data from the Mouse Genomics Institute

mortality

ncbi

Tools for querying the NCBI

ngs_tools

Genome alignment, differential expression, network analysis, and single-cell deconvolution

pnas-neuromod

randalljellis.github.io

scadie

shap

A game theoretic approach to explain the output of any machine learning model.

stringdb

Clustering and connections with STRINGdb's protein interaction database