gui/scrnaseq.py
Add CITESeq dropdown menu for QC
Updated Differential Expression to include: choice of rds object for DE; Clustering resolutions to run DE on; which test to use for DE; min fraction; min fold change; change of groups and change of contrasts. Still needs to be tested thoroughly, but at the moment will not throw errors when running QC.
Rules/scrnaQC.snakefile
Move RMarkdown QC report from Scripts to QC to match expected snakefile output for rule qcReport_scrna
Add CITESeq parameter to rule qc_scrna
Add CITESeq parameter to rule integratedBbatch
Changed rule qc_scrna to use extension-free names from groups.tab file
scrnaQC.R
Add R libraries and fixed paths
Add catch to remove “.h5” from Sample IDs in Seurat object
Add multiple clustering resolutions
Add full SingleR outputs to misc meta.data
Corrected Immune Cell Expression to DICE
Add CITESeq read in and normalization/scaling
Correct indents for readability
Add Novershtern Hematopoeitic Data to human SingleR
integrateBatches.R
Add CITESeq renormalize and rescale
Add multiple clustering resolutions
Corrected loop for multiple clustering resolutions
Corrected output to contain single output RDS that matches snakemake output
Correct indents for readability
Correct clustering parameters call (dims.use -> dims, reduction.type -> reduction)
Added catch for large datasets. Default pcs to 50 if total sample size > 50k cells
cluster.json
Changed integratedBatch params to memory=200g, time=2 days
Changed qc_scrna params to memory=150g, time = 1 day
pipeliner2.py
Added mm10 to the included list for scRNASeq
ChangeLog Feb 2020
gui/scrnaseq.py Add CITESeq dropdown menu for QC Updated Differential Expression to include: choice of rds object for DE; Clustering resolutions to run DE on; which test to use for DE; min fraction; min fold change; change of groups and change of contrasts. Still needs to be tested thoroughly, but at the moment will not throw errors when running QC.
Rules/scrnaQC.snakefile Move RMarkdown QC report from Scripts to QC to match expected snakefile output for rule qcReport_scrna Add CITESeq parameter to rule qc_scrna Add CITESeq parameter to rule integratedBbatch Changed rule qc_scrna to use extension-free names from groups.tab file
scrnaQC.R Add R libraries and fixed paths Add catch to remove “.h5” from Sample IDs in Seurat object Add multiple clustering resolutions Add full SingleR outputs to misc meta.data Corrected Immune Cell Expression to DICE Add CITESeq read in and normalization/scaling Correct indents for readability Add Novershtern Hematopoeitic Data to human SingleR
integrateBatches.R Add CITESeq renormalize and rescale Add multiple clustering resolutions Corrected loop for multiple clustering resolutions Corrected output to contain single output RDS that matches snakemake output Correct indents for readability Correct clustering parameters call (dims.use -> dims, reduction.type -> reduction) Added catch for large datasets. Default pcs to 50 if total sample size > 50k cells
cluster.json Changed integratedBatch params to memory=200g, time=2 days Changed qc_scrna params to memory=150g, time = 1 day
pipeliner2.py Added mm10 to the included list for scRNASeq