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af_bootcamp

alphafold

Open source code for AlphaFold.

aneva-dot

Tests Allelic Expression data for extreme imbalance w.r.t. population

ccm_python_bootcamp

Instructions and material related to 2023 CCM introduction to python bootcamp

cellranger

10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

clin_seqr

a shiny app to visualize clinical RNA-seq and compare to GTEX

clinpy

simple database and methods to combine clinical RNA-Seq data

colabfold

Making Protein folding accessible to all via Google Colab!

comp_on_rnaseq

Compute ontarion rna seq lecture necessary files

crg2

Research pipeline for exploring clinically relevant genomic variants

d2l-en

Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 300 universities from 55 countries including Stanford, MIT, Harvard, and Cambridge.

debrowser

Differential Count Data Analysis Toolbox

django-jazzmin

Jazzy theme for Django

ed_notes_scripts

electron_shinyapp_deployment

geminr

access to a gemini database through shiny, with a mini job schedules all within sqlite3

gtex-pipeline

GTEx Consortium data production and analysis pipelines

gtex_hpf

under heavy dev trying to replicate gtex pipeline for reproducibility

labkey_docker

Dockerfile for Labkey 18.1 others can be installed just by changing the version names

masif_compare

implementation of masif pipeline for surface comparison

meningioma

Shiny app for meningioma data

parallelfold

Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures

parse_pileup

Parse pileup files, generate consensus fasta and calculate heteroplasmy per nucleotide

pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.

pytxdb

Package to create and query R's txdb-esque database with some additional features

rblast

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

ribofootprintr

Fast data processing for ribosome footpring profiling experiments from bam files

rnaseq_lecture

rnaseq_snake

basic snakefile for RNA-Seq in active development

rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization