OHSU CEDAR's repositories
qupath_monaillabel_plugin
QuPath - Bioimage analysis & digital pathology
dynamical-cell-systems-group
Data analysis and data handling pipelines for live-cell imaging, work in progress.
SlurmStats
Script to parse through sacct outputs
ohsu-cedar-comp-hub.github.io
A work-in-progress reference for CEDAR
cfRNA-seq-pipeline-Ngo-manuscript-2019
This pipeline contains the data processing steps used for Thuy Ngo's 2019 cell-free RNA manuscript
causal-path-pipeline
A computational method to generate causal explanations for proteomic profiles using prior mechanistic knowledge in the literature, as recorded in cellular pathway maps.
ChIP-seq-pipeline
Chromatin immunoprecipitation sequencing analysis pipeline.
exon-centric-pipeline
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.
asxl1
Understanding the mechanisms of leukemicprogression in ASXL1 mutant clonal hematopoiesis through single cell-omics and novel mouse models
miRNA-pipeline
This is a pipeline to run basic miRNA processing via miRge2.0.
cfRNA-seq-pipeline
Pipeline to assess quality of Omics datasets
Bulk-RNA-seq-pipeline-SE
This is a pipeline to run basic RNA-seq analysis for single-end data.