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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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Support 5' libraries
#79
jashapiro
closed
2 years ago
2
Minor fixes to naming of flag for --include-introns in cellranger workflow
#78
allyhawkins
closed
3 years ago
0
Fixed a minor error in where the mito gene list is output in the reference fasta script
#77
allyhawkins
closed
3 years ago
0
Add --include-introns for cellranger workflow
#76
allyhawkins
closed
3 years ago
2
Modify index building workflows to include pre mRNA index
#75
allyhawkins
closed
3 years ago
0
Add alternative analysis of our spliced vs. ensembl
#74
jashapiro
closed
3 years ago
3
Comparison of Reference File Generation
#73
allyhawkins
closed
3 years ago
1
Add --include-introns as option to cellranger workflow
#72
allyhawkins
closed
3 years ago
0
Add 10X support to alevin and alevin-fry and --sketch option
#71
jashapiro
closed
3 years ago
0
Update cellranger to allow flexibility for all 10x technology
#70
allyhawkins
closed
3 years ago
0
Update cellranger to allow flexibility for all 10x technology
#69
allyhawkins
closed
3 years ago
0
Adjust reference scripts to make pre mRNA fasta needed to generate index
#68
allyhawkins
closed
3 years ago
9
Add tags to terraform resources
#67
jashapiro
closed
3 years ago
0
Make md5 check disk efficient
#66
jashapiro
closed
3 years ago
0
Add 10Xv2 support to kallisto workflow
#65
jashapiro
closed
3 years ago
2
Add --sketch option to alevin-fry workflow
#64
jashapiro
closed
3 years ago
0
Benchmarking Plan for ScPCA
#63
allyhawkins
opened
3 years ago
12
Add docker image for Alevin-fry
#62
allyhawkins
closed
3 years ago
0
Add Alevin-fry Docker Image
#61
allyhawkins
closed
3 years ago
0
Updated alevin workflows to include most recent Salmon 1.4.0/Alevin-Fry
#60
allyhawkins
closed
3 years ago
11
Benchmark Cellranger 6.0.0
#59
allyhawkins
closed
3 years ago
0
Updated nextflow workflow for cellranger 6.0.0
#58
allyhawkins
closed
3 years ago
0
Add workflow for cellranger 6.0.0
#57
allyhawkins
closed
3 years ago
0
New docker image for cellranger 6.0.0
#56
allyhawkins
closed
3 years ago
1
Create docker image for Cellranger 6.0
#55
allyhawkins
closed
3 years ago
0
Add premature RNA reference
#54
jaclyn-taroni
closed
3 years ago
0
Make the md5 process a bit more robust, and print failures
#53
jashapiro
closed
3 years ago
0
Add flexibility for 10Xv2 data
#52
jashapiro
closed
3 years ago
0
Update to salmon 1.4 & alevin-fry
#51
jashapiro
closed
3 years ago
1
Workflows for CITE-seq
#50
jashapiro
closed
3 years ago
3
Filter to 10X data
#49
jashapiro
closed
3 years ago
0
Implement TreeViz
#48
jashapiro
opened
3 years ago
0
Improve efficiency of md5 checks
#47
jashapiro
closed
3 years ago
1
Increase disk space for md5 checks
#46
jashapiro
closed
3 years ago
0
Quantification comparison, PR2 of 2: Plot mapper comparisons
#45
jashapiro
closed
3 years ago
0
Explore --mrna flag in alevin
#44
jashapiro
closed
3 years ago
3
Single Cell Data QC
#43
jashapiro
closed
2 years ago
5
Filter alevin (and other single cell workflows) to 10X data
#42
jashapiro
closed
3 years ago
0
New Workflow: Bulk RNA processing
#41
jashapiro
closed
2 years ago
1
Future Thoughts: Implement UCSC Cell Browser
#40
jashapiro
opened
3 years ago
0
Quantification comparison, PR 1 of 2: Read and standardize quantifiers to SingleCellExperiment objects
#39
jashapiro
closed
3 years ago
0
Make the main readme informative
#38
jashapiro
closed
3 years ago
1
Update top level README.md
#37
jashapiro
closed
3 years ago
0
Dockerfile update (remove install2.r)
#36
jashapiro
closed
3 years ago
0
Compare mappers and pseudomappers
#35
jashapiro
closed
3 years ago
5
Add cellranger mapping workflow
#34
jashapiro
closed
3 years ago
0
Use Launch Templates for AWS Batch configuration
#33
jashapiro
closed
3 years ago
0
Use Launch Templates for AWS Batch configuration
#32
jashapiro
closed
3 years ago
1
Add cellranger index script
#31
jashapiro
closed
3 years ago
4
Use metadata to get individual run info
#30
jashapiro
closed
3 years ago
1
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