Repositories list

• scMKL

  Public
  Python package for single-cell analysis with multiple kernel learning.

  analysissingle-cellkernel-learning+ 2

  analysissingle-cellkernel-learningcell-type-classificationmultiomics

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•77 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• Bulk-RNA-seq-pipeline-PE

  Public
  R

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• monailabel_cedar_app

  Public
  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jun 1, 2026Jun 1, 2026

• HOP_CHIP

  Public
  Snakemake workflows used to analyze genomic data (CHIP HOP purposes)

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated May 7, 2026May 7, 2026

• miniMTI

  Public
  Code for a deep learning model capable of identifying optimal reduced CyCIF marker panels and imputing additional markers

  Python

  •

  Other

  •00 forks•66 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• ohsu-cedar-comp-hub.github.io

  Public
  A work-in-progress reference for CEDAR

  Ruby

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• TITAN

  Public
  Alex Chitsazan's package TITAN for scRNA-seq (Topic Inference of Transcriptionally Associated Networks), an unsupervised Bayesian topic modelling based approach…

  R

  •

  GNU General Public License v3.0

  •22 forks•66 stars•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• scRNA_SMARTseq2

  Public
  HTML

  •33 forks•22 stars•00 issues•00 pull requests•Updated Feb 26, 2026Feb 26, 2026

• SlurmStats

  Public
  Tools to study sacct data to optimize Slurm Jobs

  Shell

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jan 28, 2026Jan 28, 2026

• AMLClock

  Public
  Snakemake workflows for analyzing DNA methylation. The first is for demultiplexing, trimming and aligning sequencing data. The second is for merging, deduplicat…

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Jan 6, 2026Jan 6, 2026

• journal-club

  Public
  Comp Bio Journal Club

  00 forks•33 stars•00 issues•00 pull requests•Updated Dec 8, 2025Dec 8, 2025

• scNMT_NOMeWorkFlow

  Public
  HTML

  •22 forks•00 stars•00 issues•00 pull requests•Updated Aug 28, 2025Aug 28, 2025

• scMKL_paper

  Public
  Repository for comparison algorithm scripts for Interpretable and Integrative Analysis of Single-Cell Multiomics with scMKL

  Python

  •

  GNU General Public License v3.0

  •11 fork•33 stars•00 issues•00 pull requests•Updated Aug 26, 2025Aug 26, 2025

• GPUOptTutorial

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 1, 2025Jul 1, 2025

• qupath_monaillabel_plugin

  Public
  QuPath - Bioimage analysis & digital pathology

  Java

  •

  GNU General Public License v3.0

  •359359 forks•55 stars•00 issues•00 pull requests•Updated Jun 27, 2025Jun 27, 2025

• 2024_ngolab_cfRNA

  Public
  R

  •

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Jun 16, 2025Jun 16, 2025

• DataMgtTools

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 3, 2025Feb 3, 2025

• dynamical-cell-systems-group

  Public
  Data analysis and data handling pipelines for live-cell imaging, work in progress.

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 15, 2025Jan 15, 2025

• WGS-nextflow-workflow

  Public
  Nextflow

  •

  Apache License 2.0

  •11 fork•33 stars•1010 issues•66 pull requests•Updated Jan 13, 2025Jan 13, 2025

• DTRON2

  Public
  DTRON Follow on project - Investigating the spatial interactions of neural and immune cells in localized prostate cancer via new image analysis tools

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 1, 2024Mar 1, 2024

• scNMT_multiomics

  Public
  HTML

  •22 forks•00 stars•00 issues•00 pull requests•Updated Dec 8, 2022Dec 8, 2022

• unidex

  Public
  python implementation of a universal demultiplexer built in mind for combinatorial indexing

  Python

  •00 forks•33 stars•22 issues•00 pull requests•Updated Dec 6, 2022Dec 6, 2022

• BC_estrogen_TITAN_paper2022

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 10, 2022Aug 10, 2022

• cfRNA-seq-pipeline-Ngo-manuscript-2019

  Public
  This pipeline contains the data processing steps used for Thuy Ngo's 2019 cell-free RNA manuscript

  R

  •55 forks•22 stars•00 issues•00 pull requests•Updated May 5, 2022May 5, 2022

• scRNAvelocity

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 14, 2022Mar 14, 2022

• collapse_antibody_library

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 26, 2021Aug 26, 2021

• causal-path-pipeline

  Public
  A computational method to generate causal explanations for proteomic profiles using prior mechanistic knowledge in the literature, as recorded in cellular pathw…

  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated Jun 22, 2021Jun 22, 2021

• ChIP-seq-pipeline

  Public
  Chromatin immunoprecipitation sequencing analysis pipeline.

  Shell

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2021Apr 14, 2021

• monocle_tools

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 4, 2021Jan 4, 2021

• exon-centric-pipeline

  Public
  Snakemake implementation of MISO (Mixture of Isoforms). MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alterna…

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 21, 2020Dec 21, 2020