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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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Issue reproducing Visium results
#83
MDLDan
opened
1 day ago
0
Merge molecules_filtered.txt into molecules_corrected.txt
#82
marcelm
closed
3 weeks ago
0
Add more colums to clone_sequences.txt and rename to clone_details.txt
#81
marcelm
closed
3 weeks ago
0
Filter out cloneIDs with deletions
#80
marcelm
opened
1 month ago
1
Fix: Filter out some additional cloneIDs
#79
marcelm
closed
1 month ago
0
Fix expected smartseq2/3 output and compare the full output
#78
marcelm
closed
1 month ago
0
Do not plot clones with just two nodes
#77
marcelm
closed
1 month ago
0
Add a read_count column to the molecules*.txt files
#76
marcelm
closed
1 month ago
0
Output the GraphViz file component by component
#75
marcelm
closed
1 month ago
0
Output the GraphViz file component by component
#74
marcelm
closed
1 month ago
0
Rename CloneGraph to CellGraph
#73
marcelm
closed
1 month ago
0
Allow "partial" matches to the exclusion list
#72
marcelm
closed
1 month ago
0
Faster processing of the exclusion list
#71
marcelm
closed
1 month ago
3
Per cell hamming
#70
Leonievb
closed
2 months ago
7
Running TREX when samples has been divided into several FASTQ files
#69
acorbat
opened
6 months ago
4
Fix plot clone graph bug
#68
acorbat
closed
6 months ago
0
Fix Jaccard Similarity Matrix construction
#67
acorbat
closed
6 months ago
1
Plotting clone graph has a division by zero problem
#66
acorbat
closed
6 months ago
0
Update dataset.py
#65
RoseString
closed
10 months ago
2
Add enhancing code of the run10x pos. argument to smartseq2/3 options
#64
Leonievb
opened
10 months ago
0
Check the code with flake8
#63
marcelm
closed
11 months ago
0
Split read_bam into two functions
#62
marcelm
closed
11 months ago
0
Reformat code with Black
#61
marcelm
closed
11 months ago
0
Some reformatting of the quality control code
#60
marcelm
closed
11 months ago
0
Link to issue/PR numbers in changelog
#59
marcelm
closed
11 months ago
0
Add clustering tests
#58
marcelm
closed
11 months ago
0
Convert test.sh tests to pytest tests
#57
marcelm
closed
11 months ago
0
Update CHANGE.md with links
#56
acorbat
closed
11 months ago
0
Filter overrepresented barcodes
#55
acorbat
closed
11 months ago
0
Fix and extend is_similar tests
#54
marcelm
closed
1 year ago
0
Dealing with deleted bases in the cloneID
#53
marcelm
opened
1 year ago
0
Filtering of short cloneIDs
#52
marcelm
opened
1 year ago
1
Adjust minimum length if --per-cell is used
#51
marcelm
opened
1 year ago
1
Improve startup time by not importing all modules all the time
#50
marcelm
closed
1 year ago
0
Refactor qc module and get rid of a warning
#49
marcelm
closed
1 year ago
0
Ensure samtools is installed for tests
#48
marcelm
closed
1 year ago
1
Add pre-commit configuration
#47
marcelm
closed
1 year ago
0
Add doublet detection
#46
marcelm
closed
1 year ago
8
Per-cell cloneID correction
#45
marcelm
closed
1 year ago
2
Make is_similar behave more consistently
#44
marcelm
closed
1 year ago
5
Tune low-complexity filtering
#43
marcelm
opened
1 year ago
0
Add low-complexity filtering
#42
marcelm
closed
11 months ago
4
Filter low-complexity cloneIDs
#41
marcelm
closed
11 months ago
2
Add a filtering option for excluding certain cloneIDs
#40
marcelm
closed
11 months ago
2
Convert NamedTuples to dataclasses
#39
marcelm
closed
1 year ago
0
Add and fix some type annotations
#38
marcelm
closed
11 months ago
0
Explain what - and 0 mean in the cloneID
#37
marcelm
closed
1 year ago
4
Per cell hamming distance
#36
acorbat
closed
1 year ago
4
Update test?
#35
acorbat
closed
12 months ago
1
correct_clone_ids looks for CloneIDs throughout the whole dataset, should it be done per cell?
#34
acorbat
closed
10 months ago
1
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