Repositories list

• Coralysis

  Public
  A multi-level integration algorithm for sensitive integration, reference-mapping, and cell state identification in single-cell data.

  scrna-seqdata-integrationproteomics

  R

  •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

• scib-pipeline

  Public
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.

  Python

  •

  MIT License

  •28•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• Coralysis-reproducibility

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• jointmodels

  Public
  R

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• Hitchhikers_Guide_scRNAseq_course

  Public
  The Hitchhiker's Guide to scRNA-seq

  integrationscrna-seq-analysisreference-mapping

  HTML

  •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

• VarSCAT

  Public
  Variant sequence context analysis tool

  Python

  •

  GNU General Public License v3.0

  •1•6•1•0•Updated Jul 5, 2024Jul 5, 2024

• Totem

  Public
  HTML

  •0•0•0•0•Updated May 29, 2024May 29, 2024

• CellRomeR

  Public
  R package for phenotypic clustering of cells from microscopy images.

  R

  •0•0•0•0•Updated Mar 13, 2024Mar 13, 2024

• ASA

  Public
  Adaptive Sequence Alignment

  Python

  •

  Other

  •0•2•0•0•Updated Mar 11, 2024Mar 11, 2024

• T1D-CyTOF-analysis

  Public
  Dataset specific analysis steps for type 1 diabetes

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 6, 2024Feb 6, 2024

• VarSCAT-analysis

  Public
  VarsSCAT analysis scripts

  R

  •0•1•0•0•Updated Dec 8, 2023Dec 8, 2023

• RolDE

  Public
  Robust longitudinal Differential Expression

  R

  •0•5•0•0•Updated Nov 27, 2023Nov 27, 2023

• scshaper-benchmarking

  Public
  R

  •0•0•1•0•Updated Aug 20, 2023Aug 20, 2023

• compbio_splicing_exercise

  Public
  Splicing hands-on exercise for COMPBIO Asia 23

  R

  •0•0•0•0•Updated Jul 11, 2023Jul 11, 2023

• PAL

  Public
  Pathway Analysis of Longitudinal data

  R

  •0•0•0•0•Updated Jun 22, 2023Jun 22, 2023

• PAL-benchmarking

  Public
  R

  •0•0•0•0•Updated Jun 20, 2023Jun 20, 2023

• PhosPiR

  Public
  R

  •0•0•0•0•Updated May 8, 2023May 8, 2023

• Totem-protocol

  Public
  protocolscrnaseqtotem-ti

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 21, 2023Apr 21, 2023

• Olissipo_hands-on_session2

  Public
  Analysing single-cell data using R

  R

  •0•2•0•0•Updated Feb 7, 2023Feb 7, 2023

• RolDE-benchmarking

  Public
  Custom codes for methods used in the study

  R

  •0•1•0•0•Updated Dec 9, 2022Dec 9, 2022

• multisubjectDSanalysis

  Public
  R

  •4•16•0•0•Updated Oct 3, 2022Oct 3, 2022

• Totem-benchmarking

  Public
  HTML

  •0•0•0•0•Updated Sep 19, 2022Sep 19, 2022

• Bioinfo_Tcell_projects_22

  Public
  EMBL-EBI scRNA Bioinformatics T cell course 2022

  course-materialstcellscrna-seq-analysis

  HTML

  •1•3•0•0•Updated Jul 7, 2022Jul 7, 2022

• PASI

  Public
  R

  •0•1•0•0•Updated Apr 14, 2022Apr 14, 2022

• Rodeo

  Public
  R

  •3•2•0•0•Updated Apr 4, 2022Apr 4, 2022

• glaDIAtor

  Public
  Tool for processing metaproteomics DDA and DIA data.

  Python

  •

  GNU General Public License v3.0

  •0•2•3•0•Updated Mar 24, 2022Mar 24, 2022

• ILoReg

  Public
  A tool for high-resolution cell population identification from single-cell RNA-seq data

  R

  •0•5•0•0•Updated Mar 8, 2022Mar 8, 2022

• semi-simulated_indel_dataset

  Public
  Semi-simulated indel dataset

  R

  •0•0•0•0•Updated Dec 24, 2021Dec 24, 2021

• scshaper

  Public
  A tool for linear trajectory inference from single-cell RNA-seq data through discrete pseudotime estimation using Shortest HAmiltonian path PERmuted clustering.

  R

  •1•5•0•0•Updated Dec 14, 2021Dec 14, 2021

• diatools

  Public
  Python

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Dec 9, 2021Dec 9, 2021