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    40 repositories

    • Benchmarking-SegmentationMethods-ST

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 18, 2026May 18, 2026

    • Learning-continuous-STranscriptomics-vector-fields-for-accurate-scalable-deep-cell-segmentation

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 14, 2026May 14, 2026

    • X-PAND

      Public
      X-PAND seeks to enable the “big leap” in correcting defective genes or instructing novel therapeutic functions into hematopoietic stem cells (HSC) by precise ge…
      Shell
      •0•0•0•0•Updated Mar 9, 2026Mar 9, 2026

    • Reusability-report-CORNETO-framework-for-knowledge-driven-multi-sample-network-inference

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • Human-neuronal-differentiation-under-AB-exposure-a-single-cell-transcriptomic-and-epigenomic-datase

      Public
      🧠 Time-resolved single-cell RNA-seq and ATAC-seq of human iPSC-derived neural progenitors differentiating into neurons, with and without amyloid-β. Dataset capt…
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • PrePR-CT

      Public
      PrePR-CT is a graph-based deep learning method designed to predict transcriptional responses to perturbations in single-cell data.
      Python
      •0•0•0•0•Updated Sep 14, 2025Sep 14, 2025

    • bcell

      Public
      Gene Regulatory Network of early B cell differentiation in Humans
      R
      •1•0•0•0•Updated Sep 1, 2025Sep 1, 2025

    • GeneSetCluster2.0

      Public
      GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis
      R
      •
      GNU General Public License v3.0
      •1•8•0•1•Updated Aug 27, 2025Aug 27, 2025

    • Transformers-for-Multiscale-Genomics

      Public
      GNU General Public License v3.0
      •7•8•0•0•Updated Feb 21, 2025Feb 21, 2025

    • A-Primer-on-Transformers-in-Single-Cell-Genomics

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Feb 21, 2025Feb 21, 2025

    • C2_ACLF_2025

      Public
      R
      •0•0•0•0•Updated Feb 2, 2025Feb 2, 2025

    • TransformersInGenomicsPapers

      Public
      A curated repository designed to serve as a comprehensive guide for researchers interested in the intersection of Transformer models and genomics. This reposito…
      Python
      •6•44•0•0•Updated Dec 18, 2024Dec 18, 2024

    • LLM_assistant_mini-review

      Public
      R
      •1•1•0•0•Updated Oct 16, 2024Oct 16, 2024

    • ClustAll

      Public
      R
      •1•1•0•0•Updated Oct 16, 2024Oct 16, 2024

    • GeneSetCluster

      Public
      a tool for summarizing and integrating gene-set analysis results
      HTML
      •
      GNU General Public License v3.0
      •4•17•0•3•Updated Aug 14, 2024Aug 14, 2024

    • scbert-reusability

      Public
      Reusability report of scBERT
      Python
      •
      GNU General Public License v3.0
      •3•14•1•0•Updated Jul 14, 2024Jul 14, 2024

    • DockerSeminar

      Public
      R
      •0•0•0•0•Updated Feb 12, 2024Feb 12, 2024

    • GSE198256_erxercise

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 30, 2024Jan 30, 2024

    • jesteg.github.io

      Public
      1•0•0•0•Updated Dec 10, 2023Dec 10, 2023

    • ClustALL_AD

      Public
      ClustALL: A robust clustering strategy for stratification of patients with acutely decompensated cirrhosis.
      R
      •0•1•0•0•Updated Nov 17, 2023Nov 17, 2023

    • BMN_characterization

      Public
      R
      •1•3•0•0•Updated Mar 5, 2023Mar 5, 2023

    • LIBRA

      Public
      Machine Translation between paired Single Cell Multi Omics Data
      HTML
      •
      GNU General Public License v3.0
      •4•6•0•0•Updated Nov 17, 2022Nov 17, 2022

    • Multiple_MM

      Public
      R
      •0•0•0•0•Updated Feb 25, 2022Feb 25, 2022

    • FANCONI

      Public
      R
      •0•0•0•0•Updated Feb 24, 2022Feb 24, 2022

    • SC_multiom

      Public
      R
      •0•0•0•0•Updated Feb 24, 2022Feb 24, 2022

    • GenomeBrowser

      Public
      0•0•0•0•Updated May 18, 2021May 18, 2021

    • RNASEQ-Pipeline

      Public
      Description of the different step in Pipeline RNAseq Single End. From fastq to count tables.
      R
      •2•1•0•0•Updated Apr 3, 2020Apr 3, 2020

    • rnaSeqBulkSnake

      Public
      bulk RNA-seq processing pipeline using DESeq2, edgeR, Voom, implemented with snakemake
      R
      •0•0•0•0•Updated Sep 10, 2019Sep 10, 2019

    • RNASEQ-Pair-end-Pipeline

      Public
      Description of the different step in Pipeline RNAseq Pair End. From fastq to count tables. Then normalize and obtain the genes highly differentiated.
      R
      •0•3•0•0•Updated Aug 21, 2019Aug 21, 2019

    • excelerate-scRNAseq

      Public
      Single RNA-seq data analysis with R (Finland, May, 2019)
      HTML
      •107•2•0•0•Updated Jul 9, 2019Jul 9, 2019
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