scholl-lab plasmicheck issues

scholl-lab / plasmicheck

Detect and quantify plasmid DNA contamination in sequencing data

MIT License

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issues

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Bug: interactive report for strongly contaminated sampels takes forever

#74 berntpopp closed 3 months ago
1
Bug: `FileNotFoundError` when loading `config.json` after installing the package via `pip install .`

#73 berntpopp closed 3 months ago
0
Feature Request: Benchmarking Dataset Creation

#72 berntpopp opened 3 months ago
2
Feature Request: Test Dataset Creation

#71 berntpopp opened 3 months ago
0
Feature Request: PEP8 Linting

#70 berntpopp closed 3 months ago
0
Feature Request: PEP8 Comments

#69 berntpopp opened 3 months ago
0
Feature Request: Normalize by Splice Junction Count

#68 berntpopp opened 3 months ago
0
Feature Request: Tables in Summary Report as Excel

#67 berntpopp closed 3 months ago
0
Feature Request: Interactive and Non-Interactive Versions of the Reports

#66 berntpopp closed 3 months ago
0
Feature Request: Add Coverage to Summary Report

#65 berntpopp opened 3 months ago
0
Feature Request: Check Coverage on Antibiotic Resistance Genes (e.g., AmpR)

#64 berntpopp opened 3 months ago
0
Bug: MD5sum File Duplicates

#63 berntpopp opened 3 months ago
0
Feature Request: Sort Tables in Summary Report

#62 berntpopp closed 3 months ago
0
Feature Request: Add Scatter Plot on Top of Respective Boxplot

#61 berntpopp opened 3 months ago
0
Refactor: Move Magic Numbers to config.json

#60 berntpopp closed 3 months ago
0
Feature Request: Update setup.py

#59 berntpopp closed 3 months ago
0
Feature request: Integrate CoverageOutsideINSERT and MismatchesNearINSERT in Summary Report

#58 berntpopp opened 3 months ago
0
Feature request: Prepare Read Scoring Output for Classification with Machine Learning

#57 berntpopp closed 3 months ago
0
Feature request: TSV Output of Tables for Summary Script

#56 berntpopp closed 3 months ago
0
Feature request: Use Summary Report Script to Calculate Variation Between Samples

#55 berntpopp closed 3 months ago
0
Feature request: Adapt Summary Matrix Plot for Large Numbers of Samples and Plasmids Dynamically

#54 berntpopp closed 3 months ago
0
Feature request: Add Favicon to HTML Output

#53 berntpopp opened 3 months ago
0
Feature request: Clean Up and Expand `keep_intermediate` Flag in Pipeline

#52 berntpopp closed 3 months ago
0
Feature request: Additional Plots for Summary Report

#51 berntpopp opened 3 months ago
0
Feature request: Correct cutoffs for exon count/CDS length (investigate methods)

#50 berntpopp opened 3 months ago
0
Feature request: Generate IGV sessions with references and BAMs

#49 berntpopp opened 3 months ago
0
Bug: Colors in report not fixed for 3 categories, it seems random

#48 berntpopp closed 3 months ago
0
Bug: BAM files are not saved in output folder

#47 berntpopp closed 3 months ago
0
Bug: Unclear range not working in sample report

#46 berntpopp closed 3 months ago
0
Refactor: logic like md5sum calculation or file name sanitizing into a utils.py

#45 berntpopp closed 3 months ago
0
Feature request: Explore machine learning for plasmid/human classification

#44 berntpopp opened 3 months ago
0
feat: Reuse spliced alignment information based on md5sum

#43 berntpopp opened 3 months ago
1
feat: Integrate images in report HTML as base64 encoded images instead of linked PNGs

#42 berntpopp closed 3 months ago
0
feat: Integrate logo (PNG) in report header

#41 berntpopp closed 3 months ago
0
feat: Add Additional classes for contamination classification

#40 berntpopp closed 3 months ago
0
feat: Reuse indices for plasmids based on md5sum

#39 berntpopp opened 3 months ago
0
feat: Implement support for other plasmid input file types like xDNA

#38 berntpopp closed 3 months ago
0
feat: Implement additional contamination check methods

#37 berntpopp closed 3 months ago
0
chore: Manage and read version from one single file

#36 berntpopp closed 3 months ago
0
docs: Better describe the tool's logic, also visually with graphs

#35 berntpopp opened 3 months ago
0
docs: Provide detailed documentation with examples

#34 berntpopp opened 3 months ago
0
feat: Add support for containerization (Docker)

#33 berntpopp opened 3 months ago
0
feat: Implement a dry-run mode

#32 berntpopp opened 3 months ago
1
feat: Automated versioning with each commit

#31 berntpopp opened 3 months ago
0
feat: Script/module to merge/generate summary reports for multiple samples and plasmids

#30 berntpopp closed 3 months ago
0
feat: Add a progress bar for long-running operations

#29 berntpopp opened 3 months ago
0
feat: Implement shifted reference to fix MAPQ0 due to identical sequence parts

#28 berntpopp opened 3 months ago
0
feat: Integrate a quality control step for input data

#27 berntpopp closed 3 months ago
0
feat: Allow customization of the output report template

#26 berntpopp opened 3 months ago
0
feat: Provide an interactive mode for easier interaction

#25 berntpopp opened 3 months ago
0