gokceneraslan

gokceneraslan's Stars

• karpathy/LLM101n

  LLM101n: Let's build a Storyteller

  30.2k2.4k01.7k

• webdataset/webdataset

  A high-performance Python-based I/O system for large (and small) deep learning problems, with strong support for PyTorch.

  Language:Python2.3k23339189

• evolutionaryscale/esm

  Language:Python1.3k2089153

• pachterlab/gget

  🧬 gget enables efficient querying of genomic reference databases

  Language:Python949107174

• laminlabs/lamindb

  A data framework for biology.

  Language:Python129237712

• mxfold/mxfold2

  MXfold2: RNA secondary structure prediction using deep learning with thermodynamic integration

  Language:Python11572034

• ludvb/xfuse

  Super-resolved spatial transcriptomics by deep data fusion

  Language:Python6734313

• ML4GLand/EUGENe

  Elucidating the Utility of Genomic Elements with Neural Nets

  Language:Jupyter Notebook654154

• thomasmaxwellnorman/Perturbseq_GI

  Code for reproducing "Exploring genetic interaction manifolds constructed from rich single-cell phenotypes"

  Language:Jupyter Notebook491222

• eQTL-Catalogue/qtlmap

  Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue

  Language:R4531313

• opentargets/gentropy

  Open Targets python framework for post-GWAS analysis

  Language:Jupyter Notebook33309

• pinellolab/EPInformer

  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization

  Language:Jupyter Notebook31118

• juliaolivieri/SpliZ_pipeline

  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis

  Language:Jupyter Notebook293119

• aertslab/CREsted

  Language:Python27771

• LieberInstitute/10xPilot_snRNAseq-human

  10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC

  Language:HTML2112129

• single-cell-genetics/singlecell_neuroseq_paper

  Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

  Language:Jupyter Notebook21616

• Genentech/decima

  Decima is a Python library to train sequence models on single-cell RNA-seq data.

  Language:Jupyter Notebook19422

• jkobject/scDataLoader

  a dataloader to work with large single cell datasets from lamindb

  Language:Jupyter Notebook15214

• FinucaneLab/Expression_Modifier_Score

  Repo for the Expression Modifier Score (EMS)

  Language:Python7521

• gagneurlab/scooby

  Language:Python71

• Helix-Research-Lab/Pool_PaRTI

  Pooling by PageRank Token Importance. This is a weighted average pooling method where the weights are derived from the internal attention matrices of the encoder.

  Language:Jupyter Notebook6100

• de-Boer-Lab/Genomic-Model-Evaluation-API

  Language:Python5201

• sayangsep/Beatrice-Finemapping

  Language:Python510

• Ahituv-lab/mprabase

  Language:Jupyter Notebook4200

• aksarkar/anmf

  Amortized NMF

  Language:Python3200

• RCHENLAB/HRCA_reproducibility

  Code and analysis from the Human Retina Cell Atlas project

  Language:Jupyter Notebook3303

• BiocPy/cellarr

  Store collections of experimental data based on TileDB

  Language:Python23101

• RiboBase/reference_homo-sapiens

  RiboFlow reference for Human

  1

• seanken/ASE_pipeline

  Our basic allele specific analysis pipeline for single nuclei data, based on nextflow

  Language:Java1100

• seanken/scAlleleExpression

  An R package for SNP level allelic expression analysis of single cell or nuclei data.

  Language:R1200