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NEWS.txt
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NEWS.txt
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##########################
#Changes to Version 1.0.0
#########################
Data Set Changes
* Added GSE168844, GSE211504, GSE212217, GSE215219, GSE227708, GSE242477
Processing Data Workflow Changes
* Reprocessed all data for Seurat v5
* Added Azimuth for automated annotation
* Refined issues with PRJNA705464 and colorectal sample names
To Do List:
* Single cell object representation with all T cells
* Finalized clustering
* Annotate clusters
* Trex Dimensionall Reduction
##########################
#Changes to Version 0.0.6
#########################
Data Set Changes
* Added GSE195486, GSE200996, GSE201425, GSE213243
Processing Data Workflow Changes
* Added deCoupler code for gene network analysis
* After testing common integration pipelines, added scArches - SCVI integration
* Removed old integration code
To Do List:
* Make central T object with latent dimensions from searches
* Finalized clustering
* Annotate clusters
* Trex Dimensionall Reduction
##########################
#Changes to Version 0.0.5
#########################
Data Set Changes
* Removed intermediate T cell Seurat Objects
* Added GSE164522
Processing Data Workflow Changes
* Updated summarizeData to work with absence of defined T cell Seurat Objects
##########################
#Changes to Version 0.0.4
#########################
Data Set Changes
* Intermediate R objects for all cells, only T cells, and TCRs will be saved in the /processedData folder
* Began parsing of combined public data sets that do not have the CellRanger outputs, the pre-processed data will be stored in processedData/combinedDataSets
* Added EGAS00001004809, GSE179994, GSE181061
Processing Data Workflow Changes
* Reprocessed all sequencing runs with updated pipeline under Processing_Utility.Rmd
* Updated ProjecTIL version and incorporated the scGate package for filtering
##########################
#Changes to Version 0.0.4
#########################
Data Set changes
* Re-annotated the different patient designations, some issues in previous version.
Processing Data Workflow Changes
* UMAP based on 20 Harmony dimensions instead of 15
* Upgraded to scRepertoire 1.3.4 and re-did the adding of the TCR data.
##########################
#Changes to Version 0.0.3
#########################
Data Set changes
* Removed GSE144469 - derived from colon pinch biopsies, not colorectal cancer (error in wen scrapper)
##########################
#Changes to Version 0.0.2
#########################
Administrative Changes
* Added NEWS file
* Removed intermediate "filtered_seuratObjects.rds" from code and stored
* Added summaryInfo directory for session info, sample directory, cohort summary
* Placed input/output of projectil and SingleR in new annotation folder
* Updated Readme to include table and corresponding link changes
Processing Data Workflow Changes
* Added filter for nFeature > 100 to initial filter steps
* Fixed issue with DICE annotation (not save correctly)
* Modified consensus annotation to accommodate DICE change
* UMAP based on 15 Harmony dimensions instead of 20
Other Code Changes
* Initial script for cohort addition (Adding Cohort) - has been run through twice