Repositories list

• flexynesis_manuscript

  Public
  All publication material relevant for the manuscript describing the flexynesis software package

  R

  •0•1•0•0•Updated Feb 13, 2025Feb 13, 2025

• VoltRon

  Public
  Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration

  R

  •

  Other

  •10•48•2•0•Updated Feb 13, 2025Feb 13, 2025

• flexynesis

  Public
  A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner

  Python

  •

  Other

  •7•31•11•0•Updated Feb 10, 2025Feb 10, 2025

• anglemania

  Public
  Improved feature extraction for scRNA-seq dataset integration.

  R

  •

  Artistic License 2.0

  •0•0•19•0•Updated Feb 10, 2025Feb 10, 2025

• flexynesis-benchmarks

  Public
  Comprehensive continuous benchmarking of tools for multi-omics data integration

  Python

  •1•1•2•0•Updated Jan 30, 2025Jan 30, 2025

• ImageArray

  Public
  R

  •1•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• compgen

  Public
  1•0•0•0•Updated Dec 28, 2024Dec 28, 2024

• pigx_rnaseq

  Public
  Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline

  snakemakepipelinernaseq+ 2guixreproducibility

  Python

  •

  GNU General Public License v3.0

  •12•21•23•0•Updated Dec 27, 2024Dec 27, 2024

• oncotrialLLM

  Public
  Python

  •0•2•0•0•Updated Dec 26, 2024Dec 26, 2024

• ZarrDataFrame

  Public
  R

  •

  MIT License

  •1•0•0•0•Updated Dec 15, 2024Dec 15, 2024

• ZarrArray

  Public
  Zarr backend for DelayedArray objects

  R

  •1•2•3•0•Updated Dec 15, 2024Dec 15, 2024

• tibanna-bimsb

  Public
  Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

  Python

  •

  MIT License

  •28•0•0•0•Updated Dec 5, 2024Dec 5, 2024

• pigx_scrnaseq

  Public
  Pipeline for analysis of Dropseq single cell data

  guixsnakemake-workflowsdropseq+ 1single-cell-rna-seq

  Python

  •6•10•28•0•Updated Nov 14, 2024Nov 14, 2024

• ikarus

  Public
  Identifying tumor cells at the single-cell level using machine learning

  machine-learningbioinformaticscancer-genomics+ 1single-cell

  HTML

  •

  MIT License

  •12•47•1•0•Updated Nov 10, 2024Nov 10, 2024

• HDF5DataFrame

  Public
  R

  •

  MIT License

  •1•0•0•0•Updated Nov 3, 2024Nov 3, 2024

• medLLMbenchmark

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Oct 21, 2024Oct 21, 2024

• CompassDock

  Public
  Official Implementation of CompassDock

  drug-discoverymolecular-biologyprotein-ligand-interactions+ 3molecular-dockingdrug-target-interactionsbinding-affinity

  Python

  •

  Other

  •3•18•0•0•Updated Oct 8, 2024Oct 8, 2024

• mergenstudio

  Public
  R

  •

  Other

  •1•4•0•0•Updated Sep 13, 2024Sep 13, 2024

• pigx_bsseq

  Public
  bisulfite sequencing pipeline from fastq to methylation reports

  bioinformaticsguixreproducibility+ 2snakemakepipeline

  Python

  •

  GNU General Public License v3.0

  •4•11•45•0•Updated Sep 12, 2024Sep 12, 2024

• mergen

  Public
  AI-Driven Code Generation, Explanation and Execution for Data Analysis

  R

  •

  Other

  •3•15•0•0•Updated Sep 11, 2024Sep 11, 2024

• pigx_docs

  Public
  Documentation for PiGx

  documentationbioinformaticspipelines+ 2reproducibilitypigx

  JavaScript

  •6•3•0•1•Updated Aug 7, 2024Aug 7, 2024

• spatialNetSmooth

  Public
  R

  •0•1•1•0•Updated Aug 5, 2024Aug 5, 2024

• scregseg

  Public
  Single-cell regulatory landscape segmentation

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•5•1•1•Updated Aug 2, 2024Aug 2, 2024

• spatialNetSmooth_scripts

  Public
  R

  •0•1•0•0•Updated Jul 30, 2024Jul 30, 2024

• scmaui-experiments

  Public
  Tutorials for scMaui

  integrationsingle-cellvariational-autoencoder+ 1multiomics

  Jupyter Notebook

  •

  Other

  •0•1•0•0•Updated Jun 17, 2024Jun 17, 2024

• pigx-common

  Public
  Common infrastructure used by all PiGx pipelines

  Python

  •

  GNU General Public License v3.0

  •1•0•2•1•Updated May 23, 2024May 23, 2024

• netSmooth

  Public
  netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

  bioinformaticsgenomicssingle-cell

  HTML

  •6•27•5•0•Updated May 15, 2024May 15, 2024

• pigx_chipseq

  Public
  Pipeline for Analysis of ChIP-Seq data

  snakemakepipelineguix+ 2reproducibilitychipseq

  Python

  •

  GNU General Public License v3.0

  •10•11•67•1•Updated May 8, 2024May 8, 2024

• rcas-web

  Public
  Web interface for RCAS

  JavaScript

  •

  GNU Affero General Public License v3.0

  •0•1•0•0•Updated May 8, 2024May 8, 2024

• bimsbbioinfo.github.io

  Public
  website for the platform

  HTML

  •12•3•0•4•Updated May 3, 2024May 3, 2024