Pinned Repositories
2024_ngolab_cfRNA
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.
cfRNA-seq-pipeline
Pipeline to assess quality of Omics datasets
cfRNA-seq-pipeline-Ngo-manuscript-2019
This pipeline contains the data processing steps used for Thuy Ngo's 2019 cell-free RNA manuscript
scRNA-tools
This repository includes many single-cell R scripts for analysis and visualization single-cell data
scRNA_SMARTseq2
scRNAvelocity
TITAN
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
unidex
python implementation of a universal demultiplexer built in mind for combinatorial indexing
WGS-nextflow-workflow
ohsu-cedar-comp-hub's Repositories
ohsu-cedar-comp-hub/TITAN
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
ohsu-cedar-comp-hub/unidex
python implementation of a universal demultiplexer built in mind for combinatorial indexing
ohsu-cedar-comp-hub/WGS-nextflow-workflow
ohsu-cedar-comp-hub/cfRNA-seq-pipeline-Ngo-manuscript-2019
This pipeline contains the data processing steps used for Thuy Ngo's 2019 cell-free RNA manuscript
ohsu-cedar-comp-hub/2024_ngolab_cfRNA
ohsu-cedar-comp-hub/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.
ohsu-cedar-comp-hub/cfRNA-seq-pipeline
Pipeline to assess quality of Omics datasets
ohsu-cedar-comp-hub/DTRON2
DTRON Follow on project - Investigating the spatial interactions of neural and immune cells in localized prostate cancer via new image analysis tools
ohsu-cedar-comp-hub/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.
ohsu-cedar-comp-hub/scRNA_SMARTseq2
ohsu-cedar-comp-hub/scRNAvelocity
ohsu-cedar-comp-hub/BC_estrogen_TITAN_paper2022
ohsu-cedar-comp-hub/AML_stroma
ohsu-cedar-comp-hub/asxl1
Understanding the mechanisms of leukemicprogression in ASXL1 mutant clonal hematopoiesis through single cell-omics and novel mouse models
ohsu-cedar-comp-hub/Bulk-RNA-seq-pipeline-SE
This is a pipeline to run basic RNA-seq analysis for single-end data.
ohsu-cedar-comp-hub/ChIP-seq-pipeline
Chromatin immunoprecipitation sequencing analysis pipeline.
ohsu-cedar-comp-hub/circRNA-pipeline
ohsu-cedar-comp-hub/collapse_antibody_library
ohsu-cedar-comp-hub/DIDA-Seq
ohsu-cedar-comp-hub/dynamical-cell-systems-group
Data analysis and data handling pipelines for live-cell imaging, work in progress.
ohsu-cedar-comp-hub/miRNA-pipeline
This is a pipeline to run basic miRNA processing via miRge2.0.
ohsu-cedar-comp-hub/monocle_tools
ohsu-cedar-comp-hub/ohsu-cedar-comp-hub.github.io
A work-in-progress reference for CEDAR
ohsu-cedar-comp-hub/qupath_monaillabel_plugin
QuPath - Bioimage analysis & digital pathology
ohsu-cedar-comp-hub/REdiscoverTE
ohsu-cedar-comp-hub/scNMT_multiomics
ohsu-cedar-comp-hub/scNMT_NOMeWorkFlow
ohsu-cedar-comp-hub/seurat_GO
ohsu-cedar-comp-hub/simulate-data
ohsu-cedar-comp-hub/SlurmStats
Script to parse through sacct outputs