Commits · 05482732a2dc18f0786db385f457a99bd7d191db · BioCellGen-public / MAGE_2020_Marker-Gene-Benchmarking · GitLab

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May 02, 2022
- Build site. · 05482732
  Jeffrey Pullin authored 2 years ago
  
  05482732
- workflowr::wflow_publish(all = TRUE, republish = TRUE) · 50bca7c1
  Jeffrey Pullin authored 2 years ago
  
  50bca7c1
Apr 28, 2022
- Add script to create manuscript figures · 24ee16ab
  Jeffrey Pullin authored 2 years ago
  
  24ee16ab
- Add script to create expert marker genes · 980fa8f9
  Jeffrey Pullin authored 2 years ago
  
  and run it in run.sh
  980fa8f9
Apr 27, 2022
- Save expert marker genes and use them in data preperation · b98019d8
  Jeffrey Pullin authored 2 years ago
  
  b98019d8
Apr 26, 2022
- Add session information to run-method script · c994d115
  Jeffrey Pullin authored 2 years ago
  
  c994d115
Apr 22, 2022
- Remove Endothelial data analysis files · 6de1aabd
  Jeffrey Pullin authored 2 years ago
  
  6de1aabd
Apr 11, 2022
- Remove the ability to set covariate in edgeR method · 934872cb
  Jeffrey Pullin authored 3 years ago
  
  934872cb
- Turn off simulation of outlier genes · dce09309
  Jeffrey Pullin authored 3 years ago
  
  dce09309
- Change simulations back to old parameters · 3434e35b
  Jeffrey Pullin authored 3 years ago
  
  3434e35b
Apr 01, 2022
- Speed up lm method · 6935d277
  Jeffrey Pullin authored 3 years ago
  
  6935d277
- Remove edgeR covariate option from benchmarking · add2bc55
  Jeffrey Pullin authored 3 years ago
  
  add2bc55
- Change dataset preperation to filter to 10,000 HVGs · db4e4d4a
  Jeffrey Pullin authored 3 years ago
  
  * Change Snakemake time allocation * Ensure simulated datasets still have 2000 genes * Change simulation parameters
  db4e4d4a
Mar 28, 2022
- Economise simulated data analyses · d9e0eb8e
  Jeffrey Pullin authored 3 years ago
  
  d9e0eb8e
- Account for NaNs in the calculation of predictive performance · 1c91d21d
  Jeffrey Pullin authored 3 years ago
  
  1c91d21d
Mar 22, 2022
- Remove FDR analysis · 4057245f
  Jeffrey Pullin authored 3 years ago
  
  4057245f
Mar 16, 2022
- Update simulation parameters · d646dd61
  Jeffrey Pullin authored 3 years ago
  
  d646dd61
Mar 15, 2022
- Remove train and test data from predictive performance results · 887f2f54
  Jeffrey Pullin authored 3 years ago
  
  887f2f54
- Add code to calculate predicitive perforamance in the Snakemake pipeline · 5d8ee361
  Jeffrey Pullin authored 3 years ago
  
  5d8ee361
Mar 10, 2022
- Run SMaSH on raw counts · 0e55c37a
  Jeffrey Pullin authored 3 years ago
  
  0e55c37a
- Update Zeisel data preperation · 240c7bc7
  Jeffrey Pullin authored 3 years ago
  
  240c7bc7
- Fix some gene names Seurat mangles · 07309681
  Jeffrey Pullin authored 3 years ago
  
  07309681
Mar 09, 2022
- Update SMART-seq3 dataset preperation · 8190c935
  Jeffrey Pullin authored 3 years ago
  
  8190c935
- Update lawlor data preperation · d454e73c
  Jeffrey Pullin authored 3 years ago
  
  d454e73c
- Change endothelial data to only have 2000 HVGs · 56dd8d52
  Jeffrey Pullin authored 3 years ago
  
  56dd8d52
Mar 08, 2022
- Add figures directory to .gitignore · c3862a0d
  Jeffrey Pullin authored 3 years ago
  
  c3862a0d
Mar 05, 2022
- Fix astrocyte logcounts · bd12d917
  Jeffrey Pullin authored 3 years ago
  
  bd12d917
- Fix harmonisation of the SMART-seq3 data · b0272cb5
  Jeffrey Pullin authored 3 years ago
  
  b0272cb5
- Remove altExps for the citesseq data · d3f74e55
  Jeffrey Pullin authored 3 years ago
  
  fixing issue with Seurat
  d3f74e55
- Fix cluster name mangling for all datasets · b734b9d8
  Jeffrey Pullin authored 3 years ago
  
  b734b9d8
Mar 01, 2022
- Add log fold-change · fdd3cac3
  Jeffrey Pullin authored 3 years ago
  
  fdd3cac3
Feb 23, 2022
- Add calculation of log fold-change for methods which do not calculate it · 7dfe8aad
  Jeffrey Pullin authored 3 years ago
  
  7dfe8aad
Feb 18, 2022
- Add first draft of predictive performance comparison · 708cfdd8
  Jeffrey Pullin authored 3 years ago
  
  708cfdd8
Feb 10, 2022

Minor adjustments to Snakefile · 4ccf3a6c

Jeffrey Pullin authored 3 years ago

* Comment out print degbugging statements
* Increase max time for running methods on real data

4ccf3a6c

Feb 09, 2022
- Add extra html files · 94016527
  Jeffrey Pullin authored 3 years ago
  
  94016527
- Build site. · 5cc008f6
  Jeffrey Pullin authored 3 years ago
  
  5cc008f6
- Refresh website · d1aca16c
  Jeffrey Pullin authored 3 years ago
  
  d1aca16c
- Remove additional unneeded analysis · 3ac9ad10
  Jeffrey Pullin authored 3 years ago
  
  3ac9ad10
Feb 08, 2022
- Remove countsimQC rmarkdown file · fcdd2eb0
  Jeffrey Pullin authored 3 years ago
  
  Will later bring back as script to be run by snakemake
  fcdd2eb0
- Add Cepo, NSForest to plot-utils · 20eca299
  Jeffrey Pullin authored 3 years ago
  
  Also add dataset names
  20eca299