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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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Add access to openscpca sim bucket
#185
jashapiro
closed
3 months ago
0
Specify library IDs to use when updating fields in scpca-meta.json
#184
allyhawkins
closed
3 months ago
0
Use named instance types for batch
#183
jashapiro
closed
4 months ago
0
Expand compute and add S3 state
#182
jashapiro
closed
5 months ago
0
Skip NA directory files
#181
jashapiro
closed
6 months ago
0
Add more vcpus to nextflow compute
#180
jashapiro
closed
6 months ago
0
Add back priority queue
#179
jashapiro
closed
6 months ago
0
Update cell type checkpoints to include the updated reference file names
#178
allyhawkins
closed
7 months ago
1
Add entries for `ref_assembly` and `star_index` to `scpca-meta.json` files
#177
allyhawkins
closed
8 months ago
1
Update script for adding new fields to `scpca-meta.json` to include assay ontology and submitter cell types
#176
allyhawkins
closed
9 months ago
5
Add assay ontology to existing `scpca-meta.json` files
#175
allyhawkins
closed
9 months ago
1
Script to add ref_mito and ref_fasta_index to scpca-meta.json
#174
allyhawkins
closed
12 months ago
2
Add `mito_file` and `ref_fasta_index` to scpca checkpoint script
#173
allyhawkins
closed
12 months ago
3
Print out sample ID with comma in scpca-meta.json
#172
allyhawkins
closed
1 year ago
1
Add script to update checkpoint directories for scpca-nf
#171
jashapiro
closed
1 year ago
2
Add Vireo image
#170
jashapiro
closed
1 year ago
0
Update Nextflow container image
#169
arkid15r
opened
2 years ago
1
Add autoscaling volumes for batch.
#168
arkid15r
closed
2 years ago
0
Test autoscaling volumes for batch
#167
jashapiro
closed
2 years ago
0
Update scripts to new metadata format
#166
jashapiro
closed
2 years ago
0
Add genetic demultiplexing comparison
#165
jashapiro
closed
2 years ago
2
Add cellhash exploration notebook
#164
jashapiro
closed
2 years ago
0
Testing quantification of spatial libraries using --sketch alignment with Alevin-fry
#163
allyhawkins
closed
2 years ago
0
Update Spatial transcriptomics benchmarking with Alevin-fry unfiltered
#162
allyhawkins
closed
2 years ago
4
Modify alevin-fry to use unfiltered mode with spatial libraries + update default indices
#161
allyhawkins
closed
2 years ago
0
Make genetic-demux into a full workflow
#160
jashapiro
closed
2 years ago
1
Include alevin-fry unfiltered for Spatial in ST benchmarking
#159
allyhawkins
closed
2 years ago
0
Modify alevin-fry workflow to run spatial transcriptomics libraries using unfiltered mode
#158
allyhawkins
closed
2 years ago
0
Rerun spatial transcriptomics benchmarking with new cellranger index
#157
allyhawkins
closed
2 years ago
0
Fix errors in spaceranger Dockerfile
#156
allyhawkins
closed
2 years ago
0
Compare genetic demultiplexing to cellhash results
#155
jashapiro
closed
2 years ago
1
Update starsolo mapping to accomodate single nuclei
#154
jashapiro
closed
2 years ago
2
Create genetic demultiplexing workflow
#153
jashapiro
closed
2 years ago
1
Add cellsnp module to genetic demux
#152
jashapiro
closed
2 years ago
1
Part 2 benchmarking spatial transcriptomics data
#151
allyhawkins
closed
2 years ago
5
Create AWS Batch job queue for running nextflow
#150
kurtwheeler
opened
2 years ago
0
Benchmarking of Spatial Transcriptomic libraries
#149
allyhawkins
closed
2 years ago
5
Add mpileup workflow
#148
jashapiro
closed
2 years ago
0
Add starsolo workflow
#147
jashapiro
closed
2 years ago
0
Add support for spatial transcriptomics libraries to Alevin-fry and Cell Ranger workflows
#146
allyhawkins
closed
2 years ago
1
Add bulk mapping with star
#145
jashapiro
closed
2 years ago
0
Add star indexing workflow
#144
jashapiro
closed
2 years ago
1
Explore spatial transcriptomics data
#143
allyhawkins
closed
2 years ago
1
Remove generic nextflow user
#142
jashapiro
closed
2 years ago
0
Add figures needed for FAQ - why did we use Alevin-fry?
#141
allyhawkins
closed
2 years ago
2
Look at combinations of filtering with miQC, mito content, and genes detected
#140
allyhawkins
closed
2 years ago
1
Explore cellhash data
#139
jashapiro
closed
2 years ago
1
add orientation switch to af permit list step
#138
jashapiro
closed
2 years ago
0
Comparison of Alevin-fry to Cellranger for 5' libraries
#137
allyhawkins
closed
2 years ago
5
Add 5' support for alevin-fry workflow
#136
allyhawkins
closed
2 years ago
0
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