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AlexsLemonade
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alsf-scpca
Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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Modify cellranger workflow to allow for 5' samples
#135
allyhawkins
closed
2 years ago
0
Explore the idea of "suggested filtering" colData and rowData fields
#134
jaclyn-taroni
opened
2 years ago
0
Quick comparison of alevin-fry to CellRanger for 5' libraries
#133
jaclyn-taroni
closed
2 years ago
3
Run 5' samples through cellranger
#131
allyhawkins
closed
2 years ago
1
Add exploration of miQC filtering
#130
allyhawkins
closed
2 years ago
8
Explore how Seurat handles AltExp data
#129
jaclyn-taroni
opened
2 years ago
0
Comparison of emptyDrops to emptyDropsCellRanger on Alevin-fry unfiltered output
#128
allyhawkins
closed
2 years ago
13
Explore genetic demultiplexing
#127
jashapiro
closed
1 year ago
4
Add scpcaTools to scpca-r image
#126
jashapiro
closed
2 years ago
1
Increase standard image disk size
#125
jashapiro
closed
2 years ago
0
Add linear regression analysis of mean gene expression across tools
#124
allyhawkins
closed
2 years ago
0
Add linear regression analysis to cr-like vs. cellranger gene comparison
#123
allyhawkins
closed
2 years ago
0
Explore use of loom files for output
#122
allyhawkins
closed
2 years ago
8
CITE-seq workflo
#120
jashapiro
closed
2 years ago
1
Update salmon to 1.5.2 and alevin-fry to 0.4.1
#119
jashapiro
closed
2 years ago
0
Update alevin-fry images to 0.4.1 (and maybe salmon?)
#118
jashapiro
closed
2 years ago
0
add barcode index files to S3
#117
jashapiro
closed
3 years ago
1
Add genes detected comparison across pre-processing tools
#116
allyhawkins
closed
2 years ago
3
Add comparison of alevin-fry resolution modes
#115
allyhawkins
closed
2 years ago
0
Create script/infrastructure to launch nextflow from a batch job
#114
jashapiro
opened
3 years ago
0
Add scpcaTools to scpca-r image
#113
jashapiro
closed
2 years ago
0
Update docker image for Alevin-fry to v0.4.0
#112
allyhawkins
closed
3 years ago
2
Test alevin-fry workflow can process multiple samples of different types at the same time
#110
allyhawkins
closed
2 years ago
0
Identify which genes are lost between alevin-fry and cellranger
#109
allyhawkins
closed
2 years ago
0
Explore post alevin-fry-unfiltered filtering strategies
#105
allyhawkins
closed
2 years ago
5
Test use of cr-like-em resolution for alevin-fry
#104
allyhawkins
closed
2 years ago
0
Update alevin-fry docker image
#103
allyhawkins
closed
3 years ago
0
Use S3 terraform backend to store state file
#102
kurtwheeler
opened
3 years ago
0
Benchmarking comparison of Alevin-fry configurations to cellranger
#101
allyhawkins
closed
3 years ago
5
Limit S3 permissions to just the buckets that are needed for SCPCA.
#100
kurtwheeler
closed
3 years ago
1
Add functions to generate QC metrics for benchmarking
#99
allyhawkins
closed
3 years ago
2
Create R package of functions used for scpca benchmarking, data import, and generation of QC metrics
#98
allyhawkins
closed
3 years ago
1
Adjust alevin to use splici index and USA mode
#97
allyhawkins
closed
3 years ago
3
Update reference scripts to make splici.fa
#96
allyhawkins
closed
3 years ago
1
Adjust reference scripts to make files needed for splici index
#95
allyhawkins
closed
3 years ago
1
Update alevin-fry docker to 0.3.0
#94
allyhawkins
closed
3 years ago
2
Update benchmarking notebooks to include correct data for SCPCR000006 alevin-fry-unfiltered-sketch
#93
allyhawkins
closed
3 years ago
0
Add additional samples to benchmarking analysis
#92
allyhawkins
closed
3 years ago
0
Make pre-mRNA index the default index for use with single-nuclei RNA seq samples
#91
allyhawkins
closed
3 years ago
0
Update SCPCR000006-alevin-fry-sketch-unfiltered run in current benchmarking analysis
#90
allyhawkins
closed
3 years ago
0
Update Cellranger for mkfastq
#89
jashapiro
closed
3 years ago
4
Add per gene level benchmarking notebook
#88
allyhawkins
closed
3 years ago
0
Incorporating snRNA-seq samples and new configurations for alevin-fry runs to time/memory benchmarking
#87
allyhawkins
closed
3 years ago
0
Incorporate snRNA-seq benchmarking samples into time/memory analysis
#86
allyhawkins
closed
3 years ago
0
Updates to Alevin-fry workflow to include unfiltered permit list
#85
allyhawkins
closed
3 years ago
0
Adjust default index references for workflows
#84
allyhawkins
closed
3 years ago
0
Add --unfiltered permit list option to alevin-fry workflow
#83
allyhawkins
closed
3 years ago
0
Preliminary benchmarking of counts output for scRNA-seq pre-processing tools
#82
allyhawkins
closed
3 years ago
14
Update alevin/kallisto workflows to use new spliced/spliced_intron references
#81
allyhawkins
closed
3 years ago
2
Preliminary benchmarking of Memory/Time footprint for pre-processing tools
#80
allyhawkins
closed
3 years ago
3
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