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UCSF-DSCOLAB
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data_processing_pipelines
A repository to store the existing pipelines to process the various CoLabs datasets
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Pipeline steps do not run after DEMUXLET
#40
amadeovezz
closed
11 months ago
0
Make outputs sync with metis model for bulk
#39
erflynn
opened
11 months ago
1
dsc pileup output always written to freemuxlet
#38
erflynn
closed
11 months ago
0
De-pool piepline for fully demultiplexed scRNAseq data
#37
dtm2451
opened
11 months ago
2
Single cell: Refactor post_qc to use new json config, and some slight refactoring
#36
amadeovezz
closed
12 months ago
3
Write csv metadata summary for all libraries
#35
erflynn
opened
12 months ago
1
add dynamic memory / input scaling
#34
erflynn
opened
12 months ago
0
make config parameters consistent across all steps
#33
erflynn
opened
12 months ago
4
Improvements to the single-cell-visualization
#32
amadeovezz
closed
11 months ago
3
Add single cell diagram for documentation purposes
#31
amadeovezz
closed
12 months ago
0
Create README.md for example-inputs
#30
erflynn
closed
12 months ago
5
Documentations updates for the single_cell_RNAseq pipeline
#29
dtm2451
closed
12 months ago
1
additional input validation
#28
erflynn
opened
12 months ago
1
option to run cellranger 7, or include-introns for older version
#27
erflynn
opened
12 months ago
0
additional options for seurat step
#26
erflynn
opened
12 months ago
0
VDJ data incorporation
#25
erflynn
opened
12 months ago
0
run both freemuxlet and demuxlet
#24
erflynn
opened
12 months ago
0
freemuxlet assign to genotype
#23
erflynn
opened
12 months ago
0
test with different data types
#22
erflynn
opened
12 months ago
0
working vcf for toy data
#21
erflynn
closed
10 months ago
1
get working with HTO multiplexed input
#20
erflynn
opened
12 months ago
0
get it to work with non-multiplexed data
#19
erflynn
opened
12 months ago
1
Updated README.md
#18
erflynn
closed
12 months ago
0
Modularized containers for the pipeline
#17
AlaaALatif
opened
1 year ago
0
Bulk rnaseq dynamic resource allocation
#16
AlaaALatif
closed
11 months ago
3
Add VDJ
#15
amadeovezz
closed
1 year ago
0
added to README installation and troubleshooting instructions
#14
tastam
closed
1 year ago
0
Updated config for larger files
#13
erflynn
closed
1 year ago
2
Bulk rnaseq pipeline -- Containerization and deployment on C4 via Slurm
#12
AlaaALatif
closed
1 year ago
0
Pre-qc V1 Refactor
#11
amadeovezz
closed
1 year ago
4
Fix: update old path for processes
#10
amadeovezz
closed
1 year ago
0
Re-org
#9
amadeovezz
closed
1 year ago
1
Update readme
#8
amadeovezz
closed
1 year ago
0
Remove legacy dir and script
#7
amadeovezz
closed
1 year ago
0
Add code from https://github.com/UCSF-DSCOLAB/sc_seq_nextflow
#6
amadeovezz
closed
1 year ago
0
v0: Initial computational pipeline for genotyping and expression analysis
#5
AlaaALatif
closed
1 year ago
3
Move parameters to configuration file, add run script
#4
erflynn
opened
2 years ago
0
Move container and index/reference paths to a separate config file
#3
arkal
closed
1 year ago
0
Update tool version and parameters (if any)
#2
arkal
closed
1 year ago
0
(WIP) update most packages used
#1
dtm2451
closed
2 years ago
1
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