issues
search
scholl-lab
/
plasmicheck
Detect and quantify plasmid DNA contamination in sequencing data
MIT License
0
stars
0
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Bug: interactive report for strongly contaminated sampels takes forever
#74
berntpopp
closed
3 weeks ago
1
Bug: `FileNotFoundError` when loading `config.json` after installing the package via `pip install .`
#73
berntpopp
closed
1 month ago
0
Feature Request: Benchmarking Dataset Creation
#72
berntpopp
opened
1 month ago
2
Feature Request: Test Dataset Creation
#71
berntpopp
opened
1 month ago
0
Feature Request: PEP8 Linting
#70
berntpopp
closed
3 weeks ago
0
Feature Request: PEP8 Comments
#69
berntpopp
opened
1 month ago
0
Feature Request: Normalize by Splice Junction Count
#68
berntpopp
opened
1 month ago
0
Feature Request: Tables in Summary Report as Excel
#67
berntpopp
closed
1 month ago
0
Feature Request: Interactive and Non-Interactive Versions of the Reports
#66
berntpopp
closed
1 month ago
0
Feature Request: Add Coverage to Summary Report
#65
berntpopp
opened
1 month ago
0
Feature Request: Check Coverage on Antibiotic Resistance Genes (e.g., AmpR)
#64
berntpopp
opened
1 month ago
0
Bug: MD5sum File Duplicates
#63
berntpopp
opened
1 month ago
0
Feature Request: Sort Tables in Summary Report
#62
berntpopp
closed
1 month ago
0
Feature Request: Add Scatter Plot on Top of Respective Boxplot
#61
berntpopp
opened
1 month ago
0
Refactor: Move Magic Numbers to config.json
#60
berntpopp
closed
1 month ago
0
Feature Request: Update setup.py
#59
berntpopp
closed
1 month ago
0
Feature request: Integrate CoverageOutsideINSERT and MismatchesNearINSERT in Summary Report
#58
berntpopp
opened
1 month ago
0
Feature request: Prepare Read Scoring Output for Classification with Machine Learning
#57
berntpopp
closed
1 month ago
0
Feature request: TSV Output of Tables for Summary Script
#56
berntpopp
closed
1 month ago
0
Feature request: Use Summary Report Script to Calculate Variation Between Samples
#55
berntpopp
closed
1 month ago
0
Feature request: Adapt Summary Matrix Plot for Large Numbers of Samples and Plasmids Dynamically
#54
berntpopp
closed
1 month ago
0
Feature request: Add Favicon to HTML Output
#53
berntpopp
opened
1 month ago
0
Feature request: Clean Up and Expand `keep_intermediate` Flag in Pipeline
#52
berntpopp
closed
4 weeks ago
0
Feature request: Additional Plots for Summary Report
#51
berntpopp
opened
1 month ago
0
Feature request: Correct cutoffs for exon count/CDS length (investigate methods)
#50
berntpopp
opened
1 month ago
0
Feature request: Generate IGV sessions with references and BAMs
#49
berntpopp
opened
1 month ago
0
Bug: Colors in report not fixed for 3 categories, it seems random
#48
berntpopp
closed
1 month ago
0
Bug: BAM files are not saved in output folder
#47
berntpopp
closed
1 month ago
0
Bug: Unclear range not working in sample report
#46
berntpopp
closed
1 month ago
0
Refactor: logic like md5sum calculation or file name sanitizing into a utils.py
#45
berntpopp
closed
1 month ago
0
Feature request: Explore machine learning for plasmid/human classification
#44
berntpopp
opened
1 month ago
0
feat: Reuse spliced alignment information based on md5sum
#43
berntpopp
opened
1 month ago
1
feat: Integrate images in report HTML as base64 encoded images instead of linked PNGs
#42
berntpopp
closed
1 month ago
0
feat: Integrate logo (PNG) in report header
#41
berntpopp
closed
1 month ago
0
feat: Add Additional classes for contamination classification
#40
berntpopp
closed
1 month ago
0
feat: Reuse indices for plasmids based on md5sum
#39
berntpopp
opened
1 month ago
0
feat: Implement support for other plasmid input file types like xDNA
#38
berntpopp
closed
1 month ago
0
feat: Implement additional contamination check methods
#37
berntpopp
closed
1 month ago
0
chore: Manage and read version from one single file
#36
berntpopp
closed
1 month ago
0
docs: Better describe the tool's logic, also visually with graphs
#35
berntpopp
opened
1 month ago
0
docs: Provide detailed documentation with examples
#34
berntpopp
opened
1 month ago
0
feat: Add support for containerization (Docker)
#33
berntpopp
opened
1 month ago
0
feat: Implement a dry-run mode
#32
berntpopp
opened
1 month ago
1
feat: Automated versioning with each commit
#31
berntpopp
opened
1 month ago
0
feat: Script/module to merge/generate summary reports for multiple samples and plasmids
#30
berntpopp
closed
1 month ago
0
feat: Add a progress bar for long-running operations
#29
berntpopp
opened
1 month ago
0
feat: Implement shifted reference to fix MAPQ0 due to identical sequence parts
#28
berntpopp
opened
1 month ago
0
feat: Integrate a quality control step for input data
#27
berntpopp
closed
1 month ago
0
feat: Allow customization of the output report template
#26
berntpopp
opened
1 month ago
0
feat: Provide an interactive mode for easier interaction
#25
berntpopp
opened
1 month ago
0
Next