Amit-H's Stars
karpathy/nanoGPT
The simplest, fastest repository for training/finetuning medium-sized GPTs.
run-llama/llama_index
LlamaIndex is a data framework for your LLM applications
kuchin/awesome-cto
A curated and opinionated list of resources for Chief Technology Officers, with the emphasis on startups
evolutionaryscale/esm
mosaicml/streaming
A Data Streaming Library for Efficient Neural Network Training
evo-design/evo
Biological foundation modeling from molecular to genome scale
nextflow-io/awesome-nextflow
A curated list of nextflow based pipelines
opencobra/cobrapy
COBRApy is a package for constraint-based modeling of metabolic networks.
xuranw/MuSiC
Multi-subject Single Cell Deconvolution
HadrienG/InSilicoSeq
:rocket: A sequencing simulator
egeulgen/pathfindR
pathfindR: Enrichment Analysis Utilizing Active Subnetworks
immunogenomics/symphony
Efficient and precise single-cell reference atlas mapping with Symphony
Bioinformatics-Research-Network/skill-assessments
Training requirements for joining projects
nf-core/funcscan
(Meta-)genome screening for functional and natural product gene sequences
AuReMe/metage2metabo
From annotated genomes to metabolic screening in large scale microbiotas
victoriapascal/gutsmash
gutSMASH
BergmannLab/MONET
MONET : MOdularising NEtwork Toolbox - https://doi.org/10.1093/bioinformatics/btaa236
cultivarium/GenomeSPOT
Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome
KenLauLab/dropkick
Automated cell filtering for single-cell RNA sequencing data
Jiaxin-Fan/MuSiC2
cell type deconvolution for multi-condition bulk RNA-seq data
bedapub/splicekit
splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
fogellab/multiWGCNA
an R package for deep mining gene co-expression networks in multi-trait expression data
grexor/pybio
pybio is a comprehensive Python framework designed to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs.
pieterjanvc/seq2mgs
A pipeline for generating custom metagenomes from existing FASTQ files
micom-dev/media
Environmental growth media for MICOM.
bedapub/space-microbe
micom-dev/databases
Workflows and input data for the construction of the standard MICOM model databases.
resendislab/micom_study
Additional materials for the micom manuscript.
danobohud/clusTCR
CDR3 clustering module providing a new method for fast and accurate clustering of large data sets of CDR3 amino acid sequences, and offering functionalities for downstream analysis of clustering results.
jiqingxiaoxi/NeSSMt
metatranscriptome simulation