tdfair's Stars
jzhoulab/puffin
deep learning-inspired explainable sequence model for transcription initiation
jzhoulab/puffin_manuscript
meta-llama/llama3
The official Meta Llama 3 GitHub site
evo-design/evo
Biological foundation modeling from molecular to genome scale
mlabonne/llm-course
Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.
marbl/Primates
Complete assemblies of non-human primate genomes
gpp-rnd/rs3
Package to Score Sequences using Rule Set 3
noamteyssier/sgcount
A flexible and fast sgRNA counter from FASTQ Files
tavareshugo/tutorial_DESeq2_contrasts
GabrielHoffman/dreamlet_analysis
Analysis code and results for dreamlet
UCSF-Chang-Lab-BRAVO/multimodal-decoding
Code associated with the paper titled "A high-performance neuroprosthesis for speech decoding and avatar control" , published in Nature in 2023.
noamteyssier/idea
Integrated Differential Expression and Annotation
chrelli/bioRxiv-word-template
MS Word template for styling a manuscript for a bioRxiv submission
MarioniLab/miloR
R package implementation of Milo for testing for differential abundance in KNN graphs
noamteyssier/cshift
A tool to perform cluster enrichment/depletion analyses
MarioniLab/miloDE
Framework for sensitive DE testing (using neighbourhoods)
pachterlab/BGP_2023
jnothman/UpSetPlot
Draw UpSet plots with Matplotlib
kaizhang/SnapATAC2
Single-cell epigenomics analysis tools
HYsxe/PRINT
nlp-with-transformers/notebooks
Jupyter notebooks for the Natural Language Processing with Transformers book
sanderlab/scPerturb
scPerturb: A resource and a python/R tool for single-cell perturbation data
csoneson/conquer_comparison
Code for evaluation of differential expression methods in single-cell RNA-seq data
thomasmaxwellnorman/Perturbseq_GI
Code for reproducing "Exploring genetic interaction manifolds constructed from rich single-cell phenotypes"
shendurelab/tafka-crisprQTL
Code associated with tafka-crisprQTL (Gasperini, et al. 2019)
noamteyssier/adpbulk
pseudobulking on an AnnData object
karpathy/nn-zero-to-hero
Neural Networks: Zero to Hero
BenLangmead/comp-genomics-class
Code and examples for JHU Computational Genomics class
broadinstitute/picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
jsh58/Genrich
Detecting sites of genomic enrichment