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hubmapconsortium
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hra-workflows-runner
hra-workflows-runner: Pipeline to download, annotate, and summarize experimental data using hra-workflows
MIT License
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Update popv.csv
#38
emquardokus
opened
3 days ago
1
popV crosswalk for heart lists hepatocyte (liver)
#37
andreasbueckle
opened
1 month ago
4
Compare CellTypist results
#36
andreasbueckle
opened
3 months ago
0
Rename hra-workflows-runner outputs according to new nomenclature (sc-transcriptomics/sc-proteomics)
#35
andreasbueckle
opened
5 months ago
0
Rename crosswalks to linkage-tables everywhere
#34
bherr2
closed
5 months ago
1
added 2 level tonsil; some cells unmapped
#33
emquardokus
closed
6 months ago
0
2 levels of Azimuth Adipose ref mapped
#32
emquardokus
closed
6 months ago
0
Add metadata column: `dataset_cell_count` and `dataset_gene_count`
#31
andreasbueckle
closed
6 months ago
1
Add metadata column to bulk-dataset-metadata.csv with sn vs sc and assay type
#30
andreasbueckle
opened
6 months ago
1
405 error with cellxgene
#29
vickydaiya
closed
6 months ago
1
Need documentation on how to access Slurm output
#28
andreasbueckle
opened
8 months ago
2
hubmap metadata updates
#27
vickydaiya
closed
9 months ago
0
gtex metadata initial iteration complete
#26
vickydaiya
closed
9 months ago
0
captures more metadata for hubmap, cellxgene and gtex
#25
vickydaiya
closed
9 months ago
0
Rename top level datasets to collections
#24
bherr2
opened
9 months ago
0
Add script to concatenate all dataset metadata for a dataset listing
#23
bherr2
closed
9 months ago
0
Add script to concatenate all cell summaries for a dataset listing
#22
bherr2
closed
9 months ago
0
Listing creation
#21
axdanbol
closed
9 months ago
0
added donor_iri to HuBMAP metadata
#20
vickydaiya
closed
9 months ago
0
tissue-donor pairs implemented for cellxgene
#19
vickydaiya
closed
9 months ago
0
gets sample iri for HuBMAP data
#18
vickydaiya
closed
10 months ago
0
adds organ in summary for successfully downloaded datasets
#17
vickydaiya
closed
10 months ago
0
captures more metadata for cellxgene datasets
#16
vickydaiya
closed
10 months ago
0
captures more metadata for GTEx datasets
#15
vickydaiya
closed
10 months ago
0
captures more metadata for HuBMAP data
#14
vickydaiya
closed
10 months ago
0
minor fixes for running the pipeline
#13
vickydaiya
closed
10 months ago
0
downloads expr.h5ad and adjusts X matrix for HuBMAP data
#12
vickydaiya
closed
10 months ago
0
Document everything!
#11
axdanbol
opened
10 months ago
0
Translate and incorporate Vicky's listing generation code
#10
axdanbol
closed
9 months ago
0
Update annotation script to utilize run queue on slurm
#9
axdanbol
closed
9 months ago
0
Reduce ram usage by cellxgene extract dataset python script
#8
axdanbol
closed
9 months ago
0
Improve tissue to organ lookup in cellxgene
#7
axdanbol
closed
9 months ago
0
Listing creation scripts
#6
axdanbol
closed
9 months ago
2
Fix dataset IDs
#5
vickydaiya
closed
10 months ago
0
PoPV
#4
vickydaiya
closed
9 months ago
0
Azimuth
#3
vickydaiya
closed
11 months ago
0
CellXGene
#2
vickydaiya
closed
11 months ago
0
Implement cellxgene data downloading (WIP)
#1
axdanbol
closed
11 months ago
0