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frisen-lab
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TREX
Simultaneous lineage TRacking and EXpression profiling of single cells using RNA-seq
MIT License
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Quality Control plots
#33
acorbat
closed
1 year ago
9
Feature: Having Quality Control plots after running TREX
#32
acorbat
closed
1 year ago
1
Set default Jaccard threshold to 0.7
#31
marcelm
closed
1 year ago
3
Remove and flag doublets
#30
marcelm
closed
11 months ago
4
--min-length flag name and documentation is misleading
#29
Leonievb
closed
1 year ago
0
Added a Jaccard index threshold documentation section and changed a naming convention
#28
Leonievb
closed
1 year ago
0
Modifications to allow multiple BAM file input
#27
Leonievb
closed
10 months ago
10
Providing an input folder containing one BAM file per cell does not work
#26
Leonievb
closed
10 months ago
1
Automatic detection of clone_id location throws error in some cases
#25
Leonievb
opened
1 year ago
3
Document the usage of the jaccard score
#24
Leonievb
closed
1 year ago
0
Formatting
#23
Leonievb
closed
1 year ago
1
Implementation of smartseq3 positional argument
#22
Leonievb
closed
1 year ago
0
Migrate from setup.cfg to pyproject.toml
#21
marcelm
closed
1 year ago
0
Describe how to run TREX on the paper data
#20
marcelm
closed
2 years ago
0
Raw umi matrix?
#19
cnk113
closed
2 years ago
1
Factor out an add_common_arguments() function
#18
marcelm
closed
2 years ago
1
Document that --plot requires Graphviz
#17
marcelm
closed
2 years ago
0
Document `--filter-cellids` file format
#16
marcelm
closed
1 year ago
0
Describe output files created by run10x
#15
marcelm
closed
2 years ago
2
clones.txt contains a clone_id column, but it’s not the clone ID
#14
marcelm
closed
1 year ago
0
create the positional argument `Smartseq3` to allow running smartseq3 data with UMI
#13
marcelm
closed
1 year ago
0
Reconsider the name of the `annotations` folder and its contents
#12
marcelm
closed
2 years ago
5
Remove duplicated file and top-level expected/ folder
#11
marcelm
closed
2 years ago
1
The test run only gives error on folder structure when -f flag added
#10
Leonievb
closed
2 years ago
1
The --help section needs to be updated
#9
Leonievb
closed
2 years ago
3
Usage of the smartseq vs. 10x runs commands unclear
#8
Leonievb
closed
1 year ago
7
The output of the clone calling algorithm does not match R output in some cases
#7
Leonievb
closed
1 year ago
2
The documentation should show all available arguments
#6
Leonievb
closed
1 year ago
0
The test data are incomplete
#5
Leonievb
closed
1 year ago
0
Folder structure is inconsistent
#4
Leonievb
closed
2 years ago
5
A consistently documented pipeline is missing
#3
Leonievb
closed
1 year ago
0
Output table formats are inconsistent
#2
marcelm
closed
1 year ago
0
Reproducing the cloneID raw matrix
#1
cnk113
closed
2 years ago
5
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