Repositories list

• SlurmStats

  Public
  Tools to study sacct data to optimize Slurm Jobs

  Shell

  •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

• WGS-nextflow-workflow

  Public
  Nextflow

  •

  Apache License 2.0

  •1•3•13•3•Updated Oct 3, 2024Oct 3, 2024

• DataMgtTools

  Public
  Shell

  •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

• qupath_monaillabel_plugin

  Public
  QuPath - Bioimage analysis & digital pathology

  Java

  •

  GNU General Public License v3.0

  •278•0•0•0•Updated Sep 28, 2024Sep 28, 2024

• dynamical-cell-systems-group

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

  Jupyter Notebook

  •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

• TITAN

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

  R

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated Sep 5, 2024Sep 5, 2024

• scRNA_SMARTseq2

  Public
  HTML

  •2•1•0•0•Updated Aug 6, 2024Aug 6, 2024

• 2024_ngolab_cfRNA

  Public
  R

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Aug 2, 2024Aug 2, 2024

• scNMT_NOMeWorkFlow

  Public
  HTML

  •1•0•0•0•Updated Jun 28, 2024Jun 28, 2024

• 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

  •0•1•0•0•Updated Mar 1, 2024Mar 1, 2024

• ohsu-cedar-comp-hub.github.io

  Public
  A work-in-progress reference for CEDAR

  Ruby

  •1•0•0•0•Updated Sep 27, 2023Sep 27, 2023

• scNMT_multiomics

  Public
  HTML

  •1•0•0•0•Updated Dec 8, 2022Dec 8, 2022

• unidex

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

  Python

  •0•3•2•0•Updated Dec 6, 2022Dec 6, 2022

• BC_estrogen_TITAN_paper2022

  Public
  R

  •0•0•0•0•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

  •5•2•0•0•Updated May 5, 2022May 5, 2022

• scRNAvelocity

  Public
  Python

  •0•1•0•0•Updated Mar 14, 2022Mar 14, 2022

• collapse_antibody_library

  Public
  Python

  •0•0•0•0•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 pathway maps.

  Python

  •1•1•0•0•Updated Jun 22, 2021Jun 22, 2021

• ChIP-seq-pipeline

  Public
  Chromatin immunoprecipitation sequencing analysis pipeline.

  Shell

  •2•0•0•0•Updated Apr 14, 2021Apr 14, 2021

• monocle_tools

  Public
  R

  •0•0•0•0•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 alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.

  Python

  •0•1•0•0•Updated Dec 21, 2020Dec 21, 2020

• simulate-data

  Public
  Python

  •0•0•0•0•Updated Oct 13, 2020Oct 13, 2020

• REdiscoverTE

  Public
  Python

  •0•0•0•0•Updated Sep 21, 2020Sep 21, 2020

• asxl1

  Public
  Understanding the mechanisms of leukemicprogression in ASXL1 mutant clonal hematopoiesis through single cell-omics and novel mouse models

  HTML

  •0•0•0•0•Updated Jun 30, 2020Jun 30, 2020

• DIDA-Seq

  Public
  Python

  •1•0•0•0•Updated May 12, 2020May 12, 2020

• miRNA-pipeline

  Public
  This is a pipeline to run basic miRNA processing via miRge2.0.

  Python

  •0•0•0•0•Updated Mar 27, 2020Mar 27, 2020

• AML_stroma

  Public
  R

  •0•0•0•0•Updated Mar 19, 2020Mar 19, 2020

• cfRNA-seq-pipeline

  Public
  Pipeline to assess quality of Omics datasets

  R

  •4•1•0•0•Updated Feb 27, 2020Feb 27, 2020

• Bulk-RNA-seq-pipeline-SE

  Public
  This is a pipeline to run basic RNA-seq analysis for single-end data.

  R

  •4•0•0•0•Updated Feb 27, 2020Feb 27, 2020

• seurat_GO

  Public
  R

  •0•0•0•0•Updated Feb 27, 2020Feb 27, 2020