https://github.com/fertiglab/emt_ewald
Curated set of analysis scripts for single cell data from the Ewald Lab.
https://github.com/fertiglab/emt_ewald
Last synced: 6 months ago
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Curated set of analysis scripts for single cell data from the Ewald Lab.
- Host: GitHub
- URL: https://github.com/fertiglab/emt_ewald
- Owner: FertigLab
- Created: 2021-07-26T12:37:15.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2022-07-25T15:35:57.000Z (almost 4 years ago)
- Last Synced: 2025-10-25T14:41:36.675Z (8 months ago)
- Language: Jupyter Notebook
- Size: 1.91 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# EMT_Ewald
Curated set of analysis scripts for single cell data from the Ewald Lab.
### 1_CombineData.ipynb
#### Description - Joins the counts data together
##### Input
* D1-D3-D5-byHaiping/D1/filtered_feature_bc_matrix/matrix.mtx
* D1-D3-D5-byHaiping/D1/filtered_feature_bc_matrix/barcodes.tsv
* D1-D3-D5-byHaiping/D1/filtered_feature_bc_matrix/features.tsv
* D1-D3-D5-byHaiping/D3/filtered_feature_bc_matrix/matrix.mtx
* D1-D3-D5-byHaiping/D3/filtered_feature_bc_matrix/barcodes.tsv
* D1-D3-D5-byHaiping/D3/filtered_feature_bc_matrix/features.tsv
* D1-D3-D5-byHaiping/D5/filtered_feature_bc_matrix/matrix.mtx
* D1-D3-D5-byHaiping/D5/filtered_feature_bc_matrix/barcodes.tsv
* D1-D3-D5-byHaiping/D5/filtered_feature_bc_matrix/features.tsv
##### Output
* mergedAdata.h5ad
### 2_cleanData.ipynb
#### Description - Preprocesses the combined data
##### Input
* mergedAdata.h5ad
##### Output
* labelledAdata.h5ad
* data/dataMatrix.mtx'
* data/obs.csv
* data/var.csv
* rawCleanadata.h5ad
* data/dataMatrixClean.mtx
* data/obsClean.csv
* data/varClean.csv
### 3_ClusteringAfterBatchCorrection.Rmd
#### Description - Create CDS with the “clean” data. CDS is preprocessed.
##### Input
* data/dataMatrixClean.mtx
* data/obsClean.csv
* data/varClean.csv
##### Output
* intermediateData/cdsBasic.RDS
* intermediateData/cdsBasic.RDS
* data/normalizedMatrix.mtx
* intermediateData/cdsNormalizedDimReduced.rds
* intermediateData/cdsDayCorrected.RDS
### 4_EJFPreprocessingAnalysis.Rmd
#### Description - Run pseudotime for matrigel and collagen
##### Input
* intermediateData/cdsBasic.RDS
* geneList.csv
##### No Output
### 5_EJFPreprocessingAnalysis.R
#### Description - Run pseudotime for matrigel and collagen
##### Input
* cdsBasic.RDS
* geneList.csv
##### Output
* EJFPsuedotimeResults2Mar2020.Rda
### 6_PseudotimeCorrectedData.Rmd
#### Description - Process and plot the corrected data
##### Input
* intermediateData/cdsDayCorrected.RDS
* geneList.csv
##### No Output
### 7_ScanpyEMT.ipynb
#### Description - Calculate and export cell cycle
##### Input
* rawCleanadata.h5ad
* regev_lab_cellCycle_smouse.txt
* regev_lab_cellCycle_mmouse.txt
##### Output
* obs.csv
### 8_addCellCycle.Rmd
#### Description - Add cell cycle to cds objects
##### Input
* EJFPsuedotimeResults2Mar2020.Rda
* obs.csv
##### Output
* cellCycle_EJFPsuedotimeResults2Mar2020.Rda
### 9_CoGAPSData_collagen.Rmd
#### Description - Calculate top collagen genes and subset the data to those genes for CoGAPS
##### Input
* EJFPsuedotimeResults2Mar2020.Rda
##### Output
* sbstCds.rds
* countsSbstCds.rds
### 10_cogapsObjects_collagen.Rmd
#### Description - Create CoGAPS objects for the collagen gene subset
##### Input
* countsSbstCds.rds
##### Output
* emtMat.mtx
* emtParams.rds
### 11_ewald_gwCogapsAnalysis_collagen.Rmd
#### Description - Analyze CoGAPS results
##### Input
* sbstCds.rds
* CoGAPS results
##### Output
* UMAPS
* Boxplots
* patternMarkers_emtGwCogaps_20.csv
### 12_cogapsVisuals_collagen.Rmd
#### Description - Create heatmap and gene rank file for CoGAPS result
##### Input
* gwCogapsRes/emtGwCogaps_20.rds
* geneList.csv
##### Output
* emtGeneRanks.csv
### Ran gene set analysis using MSigDb
#### Input
* Pattern marker genes
#### Output
* Pathway results
### 13_Figure.Rmd
#### Description - Create the first set of figures
##### Input
* cellCycle_EJFPsuedotimeResults2Mar2020.Rda
* gwCogapsRes/emtGwCogaps_20.rds
* msigdb/emtPatterns.csv
* patternMarkers_emtGwCogaps_20.csv
* geneList.csv
* msigdb/emtPatterns.csv
* emtResults.csv
##### Output
* Figures
### 14_ChungProjection.Rmd
#### Description - Format the Chung single cell data, subset to tumor cells, run ProjectR
##### Input
* GSE75688_GEO_processed_Breast_Cancer_raw_TPM_matrix.txt
* GSE75688_final_sample_information.txt
* gwCogapsRes/emtGwCogaps_20.rds
##### Output
* HumanTumorCoGAPSprojection.rdata
* Projected pattern umaps
### 15_CoGAPSData_matrigel.Rmd
#### Description - Subset to top collagen genes for the matrigel data for CoGAPS
##### Input
* EJFPsuedotimeResults2Mar2020.Rda
* emtGwCogaps_20.rds
##### Output
* 15_sbstCdsMatrigel.rds
* 15_countsSbstCdsMatrigel.rds
### 16_cogapsObjects_matrigel.Rmd
#### Description - Create the cogaps objects for the matrigel cogaps runs
##### Input
* 15_countsSbstCdsMatrigel.rds
##### Output
* 16_sampleGeneNamesMatrigel.rdata
* 16_emtMatMatrigel.mtx
* 16_emtParamsMatrigel.rds