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https://github.com/fertiglab/pdac_atlas

Analysis workflow for all data present in our PDAC Atlas Manuscript titled, "Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma"

https://github.com/fertiglab/pdac_atlas

Science Score: 13.0%

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Repository

Analysis workflow for all data present in our PDAC Atlas Manuscript titled, "Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma"

Basic Info
  • Host: GitHub
  • Owner: FertigLab
  • Language: R
  • Default Branch: main
  • Size: 41.4 MB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 3 years ago · Last pushed almost 3 years ago
Metadata Files
Readme

README.md

PDAC_Atlas

Analysis workflow for all data present in our PDAC Atlas Manuscript titled, "Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma"

Atlas Workflow

Scripts for the creation of the atlas, and its downstream analyses can be found under the /Atlas Directory.

Data Required to follow along

  • PDAC atlas engineering051622BK.Rmd:
    1. RAW Counts from all manuscripts
  • PDAC atlas analysis051622BK.Rmd:
    1. cdscombined8SHAREDGENESQCfilteredharmonizedpreprocessedalignedmanuscriptUMAPlearn_graph.rds
  • PDACMHCIIDifferentialExprs.Rmd:
    1. cdsductSHAREDGENESQCfilteredharmonizedpreprocessedalignedmanuscriptUMAPlearngraph.rds
  • PDACCAFMHCII_DifferentialExprs.Rmd:
    1. cdscombined8SHAREDGENESQCfilteredharmonizedpreprocessedalignedmanuscriptUMAPlearn_graph.rds
  • 06222022STEELEPYSCENICHG38only.sh & DominoPDACEpCAFSTEELE_HG38only.Rmd:
    1. cdscombined8SHAREDGENESQCfilteredharmonizedpreprocessedalignedmanuscriptUMAPlearn_graph.rds
  • 06222022PENGPYSCENICHG38only.sh & DominoPDACEpCAFPENG_HG38only.Rmd:
    1. cdscombined8SHAREDGENESQCfilteredharmonizedpreprocessedalignedmanuscriptUMAPlearn_graph.rds

Mutliseq Workflow

Scripts for the analysis of the 12HR PDO-CAF Coculture scRNA-seq data can be found under the /Multiseq Directory.

Data Required to follow along

  • Preprocess_fromCore:
    1. RAW FASTQ
  • 12HMultiSeq01ProjRInflammation.Rmd:
    1. dgeData.rda
    2. epiMat-e74511f6-8a1d-4929-ab42-1cb67c5a4fb6-result-8pattern.rds
  • 12HMultiSeq02_Moffit.Rmd:
    1. 12HMultiSeqProjR_InflammationData.rda

Bulk RNAseq Workflow

Scripts for the analysis of the 3 untreated PDO-CAF bulk RNA-seq data can be found under the /Bulkseq Directory.

Data Required to follow along

  • 00ExtractSample_Names.Rmd:
    1. Raw Data Folder names
  • 01salmonQuant.sh & 01SGNovogene12202022_SalmonSetup.R:
    1. RAW FASTQ files from Novogene
  • 02SalmonQuantto_txi.Rmd:
    1. Output of Salmon.sh (Salmon_Quants/)
    2. tgMap.tsv
  • 03PDACAtlasCoGAPS_Projection.Rmd:
    1. txidataall.rds
    2. SGNovogeneAnnot.csv
    3. epiMat-e74511f6-8a1d-4929-ab42-1cb67c5a4fb6-result-8pattern.rds

Owner

  • Name: FertigLab
  • Login: FertigLab
  • Kind: organization
  • Email: ejfertig@jhmi.edu

Software projects in computational biology and bioinformatics in Elana Fertig's lab in Oncology Biostatistics and Bioinformatics at JHMI

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