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BAUDOTlab
/
scDataPipeline
Reusable standard single-cell RNA sequencing data analysis pipeline
MIT License
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add COMBINED as a configuration parameter
#71
Rumengol
closed
9 months ago
0
Feat improved rbc removal
#70
Rumengol
closed
9 months ago
0
Gene-of-Interest List Includes Genes with No Counts, Causing FeaturePlot Failure
#69
celinech
closed
6 months ago
0
Make the pipeline work on ENSid
#68
celinech
closed
9 months ago
0
Feat en sid
#67
celinech
closed
9 months ago
0
Feat docker
#66
Rumengol
closed
9 months ago
0
Pipeline works with ENSEMBL ids and map them to gene names for readab…
#65
celinech
closed
9 months ago
0
Use docker to run the pipeline
#64
Rumengol
closed
9 months ago
0
Verification of reports
#63
sevdarafatov
closed
10 months ago
0
Use docker to run the pipeline
#62
Rumengol
closed
10 months ago
0
Add sanity checks to load_parameters
#61
Rumengol
closed
7 months ago
0
Put every function out of Rmd files
#60
Rumengol
opened
10 months ago
1
Raise Error message on manualControls thresholds if group is empty
#59
Rumengol
closed
6 months ago
0
When run combine, make sure the single datasets where processed with the same parameters (normalization, do_scale, scenario, etc)
#58
Rumengol
opened
10 months ago
0
Add gene_annotation as required param to fully write if it is Ensembl IDs or gene names (not only rely on the input file; imagine the columns are in the other order, everything will work on the wrong gene_annotation)
#57
Rumengol
opened
10 months ago
1
Implement title and some output to the script 06_combineData_pipeline.Rmd (it doesn't show anything)
#56
Rumengol
opened
10 months ago
0
Make identifiable a report when it is opened
#55
Rumengol
closed
9 months ago
0
Homogeneize variable names according to a standard (snakecase, pascalcase, camelcase)
#54
Rumengol
opened
10 months ago
3
Dev: New feature to display manual annotation on Meld plots
#53
celinech
closed
10 months ago
0
Fix overwriting output file
#52
celinech
closed
10 months ago
0
save under different name the correspondance table
#51
celinech
closed
10 months ago
0
Add error handling for genes_of_interest file in 05_annotDEAviz_pipeline
#50
PhilippeBaratta
closed
8 months ago
2
BUGFIX force reticulate to use env's python
#49
celinech
closed
10 months ago
0
BUGFIX change path to input file
#48
celinech
closed
10 months ago
0
Update chunk names to all chunks and small text changes
#47
celinech
closed
10 months ago
2
Don't run the `ctrl` step for each scenarios
#46
Rumengol
closed
6 months ago
0
Print sessionInfo() at the end of each .html reports
#45
celinech
closed
11 months ago
0
Readme
#44
Rumengol
closed
11 months ago
0
Add a COMBINED boolean field in config files
#43
Rumengol
closed
9 months ago
0
[TEMP] add scenario to saved figure names
#42
Rumengol
closed
11 months ago
0
Bug fix
#41
celinech
closed
11 months ago
0
Run analyses without an atlas
#40
Rumengol
closed
10 months ago
1
Meld
#39
Rumengol
closed
11 months ago
1
change PATH_OUT_ANALYSIS and file names
#38
celinech
closed
11 months ago
0
Save matplotlib plots as pdf
#37
Rumengol
closed
9 months ago
2
Restructure the 52_figures with subfolder for each step
#36
Rumengol
opened
11 months ago
1
Bugs
#35
celinech
closed
12 months ago
1
handles the scenario list for related steps
#34
Rumengol
closed
12 months ago
0
Toml
#33
celinech
closed
1 year ago
1
Fix two bugs
#32
Rumengol
closed
1 year ago
0
Multiple scenario analysis not working
#31
celinech
closed
11 months ago
1
add scenario management to data slot
#30
Rumengol
closed
1 year ago
0
fix combine to use scale.data slot instead of data
#29
Rumengol
closed
1 year ago
0
add the config file parameter PATH_ATLAS_FILE to enable the use of mu…
#28
Rumengol
closed
12 months ago
1
fix scenario parameter in process html name
#27
Rumengol
closed
1 year ago
0
Adding titles to the UMAP plots
#26
sevdarafatov
opened
1 year ago
1
combinedD command check for null and set False as default
#25
Rumengol
closed
1 year ago
0
03_filtersControls_pipeline.Rmd typo at line 141
#24
sevdarafatov
closed
1 year ago
0
Dataset sanity check
#23
sevdarafatov
closed
1 year ago
1
Raising an error if there`s space/tab at the end of DATASET or DATASET contains a space/tab
#22
sevdarafatov
closed
1 year ago
1
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