Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / mjmlab/pyinseq issues and pull requests
#90 - Unknown argument(s): {'colour': 'green'}
Issue -
State: open - Opened by nbutyrate over 1 year ago
#89 - No module named 'importlib.metadata'
Issue -
State: open - Opened by nbutyrate over 1 year ago
#88 - Running the pipeline without sample list.
Issue -
State: closed - Opened by gaworj over 2 years ago
- 3 comments
#87 - Revise installation instructions for release 0.3.2
Pull Request -
State: closed - Opened by mandel01 over 2 years ago
- 2 comments
#86 - Installation instructions for snakelike need to include mamba
Issue -
State: closed - Opened by mandel01 over 2 years ago
- 1 comment
#85 - Summary gene table output is incorrect, only includes last entry for each gene from *genes.txt
Issue -
State: closed - Opened by mandel01 over 2 years ago
- 5 comments
Labels: bug
#84 - Add to bioconda
Issue -
State: closed - Opened by mandel01 about 3 years ago
- 1 comment
#83 - Matplotlib from conda missing baseline images when `pyinseq --test` is called
Issue -
State: open - Opened by eburgoswisc about 3 years ago
- 1 comment
#82 - Bug in PyPi project description
Issue -
State: closed - Opened by eburgoswisc about 3 years ago
- 3 comments
#81 - Final changes for 0.3.0 version to be published
Pull Request -
State: closed - Opened by eburgoswisc about 3 years ago
- 4 comments
#80 - Merging snakemake into master
Pull Request -
State: closed - Opened by eburgoswisc over 3 years ago
- 3 comments
#79 - Final changes for v0.2.1 release
Pull Request -
State: closed - Opened by eburgoswisc over 3 years ago
- 1 comment
#78 - Add new args of barcode_length and transposon_seq
Pull Request -
State: closed - Opened by eburgoswisc over 3 years ago
- 1 comment
#77 - Handling of reads that begin with TA site
Issue -
State: closed - Opened by eburgoswisc over 4 years ago
#76 - Add GFF3 option and remove extra EOL characters
Pull Request -
State: closed - Opened by mandel01 about 5 years ago
- 4 comments
#75 - Adding progress bar to demultiplex functions
Pull Request -
State: closed - Opened by eburgoswisc over 5 years ago
- 11 comments
#74 - Use Exception Class for Pyinseq specific errors
Issue -
State: closed - Opened by eburgoswisc over 5 years ago
- 3 comments
#73 - File reading in demultiplex is slow
Issue -
State: closed - Opened by eburgoswisc over 5 years ago
- 1 comment
#72 - Fix three_primeness math
Pull Request -
State: closed - Opened by mandel01 over 5 years ago
- 11 comments
#71 - three_primeness math
Issue -
State: closed - Opened by mandel01 over 5 years ago
#70 - Change N50 to T50
Pull Request -
State: closed - Opened by eburgoswisc over 5 years ago
- 3 comments
#69 - Add basic analysis functions
Pull Request -
State: closed - Opened by eburgoswisc over 5 years ago
- 4 comments
#68 - Tidy code
Pull Request -
State: closed - Opened by mandel01 almost 6 years ago
- 4 comments
#67 - Nfifty Implementation
Pull Request -
State: closed - Opened by eburgoswisc almost 6 years ago
- 5 comments
#66 - nfifty pipeline implementation and test update
Pull Request -
State: closed - Opened by eburgoswisc almost 6 years ago
#65 - Format code with black
Pull Request -
State: closed - Opened by mandel01 almost 6 years ago
- 1 comment
#64 - Map gene parameters
Pull Request -
State: closed - Opened by eburgoswisc almost 6 years ago
- 2 comments
#63 - Add map gene parameters
Pull Request -
State: closed - Opened by eburgoswisc almost 6 years ago
- 1 comment
#62 - Test Python 3.7
Pull Request -
State: closed - Opened by mandel01 almost 6 years ago
- 4 comments
#61 - Set mkdocs, mkdocs-cinder version numbers
Pull Request -
State: closed - Opened by mandel01 almost 6 years ago
#60 - Update MkDocs to the cinder theme
Pull Request -
State: closed - Opened by mandel01 almost 6 years ago
#59 - Switch from Sphinx to MkDocs
Pull Request -
State: closed - Opened by mandel01 almost 6 years ago
- 1 comment
#58 - Quality control parameters for minimum reads and left/right ratio
Pull Request -
State: closed - Opened by eburgoswisc almost 6 years ago
#57 - ReadTheDocs documentation build is failing
Issue -
State: closed - Opened by mandel01 about 6 years ago
- 1 comment
#56 - Python 3.6 support only
Pull Request -
State: closed - Opened by mandel01 about 6 years ago
- 1 comment
#55 - Add PyCharm .idea/ dir to version control
Pull Request -
State: closed - Opened by mandel01 about 6 years ago
#54 - Fix issue #52 of test_script
Pull Request -
State: closed - Opened by eburgoswisc about 6 years ago
- 4 comments
#53 - Need pypi description
Issue -
State: closed - Opened by mandel01 about 6 years ago
- 1 comment
#52 - test_pyinseq_genomeprep_script doesn't seem to work
Issue -
State: closed - Opened by mandel01 about 7 years ago
- 5 comments
Labels: bug
#51 - Improve logging and pyinseq demultiplex command
Pull Request -
State: closed - Opened by mandel01 over 7 years ago
- 1 comment
#50 - Automatically deploy docs to gh-pages
Issue -
State: closed - Opened by mandel01 over 7 years ago
#49 - Add sphinx-generated documentation
Pull Request -
State: closed - Opened by mandel01 almost 8 years ago
- 1 comment
#48 - Add code coverage configuration
Pull Request -
State: closed - Opened by mandel01 almost 8 years ago
#47 - Start analysis workflow
Pull Request -
State: closed - Opened by mandel01 almost 8 years ago
#46 - Analyze
Pull Request -
State: closed - Opened by mandel01 almost 8 years ago
#45 - Add python3 in shebang, other tidying
Pull Request -
State: closed - Opened by mandel01 almost 8 years ago
#44 - New package structure
Pull Request -
State: closed - Opened by mandel01 almost 8 years ago
#43 - The Big Package Structure Refactor
Pull Request -
State: closed - Opened by camillescott almost 8 years ago
- 2 comments
#42 - Added functionality for demultiplexed samples
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#41 - Correct asserts
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#40 - Put disruption processing in set_disruption() module
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#39 - pyinseq.py class Settings() instead of globals
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#38 - Reorganize package and tests
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#37 - Writing more informative tests and reorganizing the repo so tests can query individual functions.
Issue -
State: closed - Opened by mandel01 over 8 years ago
- 1 comment
#36 - Organized sample and summary dictionaries
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#35 - Items that need to be documented or that need better documentation
Issue -
State: closed - Opened by mandel01 over 8 years ago
- 1 comment
#34 - Python repo and bowtie location fixed
Pull Request -
State: closed - Opened by rebeldroid12 over 8 years ago
- 3 comments
#33 - Added disruption value check
Pull Request -
State: closed - Opened by biobenkj over 8 years ago
- 2 comments
#32 - Added disruption value check
Pull Request -
State: closed - Opened by biobenkj over 8 years ago
- 2 comments
#31 - Re-running previously demultiplexed samples
Issue -
State: closed - Opened by biobenkj over 8 years ago
- 3 comments
#30 - New directory generator based on experiment name
Issue -
State: closed - Opened by biobenkj over 8 years ago
- 1 comment
#29 - pip install for requirements.txt error
Issue -
State: closed - Opened by biobenkj over 8 years ago
- 1 comment
#28 - Initial logging of results but messy
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#27 - Add logdata for logging and parse bowtie output
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#26 - Add Python 3.5 Badge
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#25 - Fix path to pyinseq.py
Pull Request -
State: closed - Opened by ellarotman over 8 years ago
- 1 comment
#24 - Working .travis.yml and cleaned up imports
Pull Request -
State: closed - Opened by mandel01 over 8 years ago
#23 - Add dev branch
Issue -
State: closed - Opened by mandel01 over 8 years ago
#22 - Github displays wrong language
Issue -
State: closed - Opened by mandel01 over 8 years ago
- 3 comments
#21 - Initial thoughts for contributors guide.
Issue -
State: closed - Opened by mandel01 over 8 years ago
Labels: enhancement
#20 - Improve appearance of documentation
Issue -
State: closed - Opened by mandel01 over 8 years ago
- 6 comments
Labels: enhancement
#19 - Improve testing
Issue -
State: closed - Opened by mandel01 over 8 years ago
- 2 comments
Labels: enhancement
#18 - Improve the modular design of the pipeline
Issue -
State: closed - Opened by mandel01 over 8 years ago
- 1 comment
#17 - added numpy, pandas, matplotlib as requirements
Pull Request -
State: closed - Opened by mandel01 almost 9 years ago
#16 - Bundle bowtie directly in the package
Pull Request -
State: closed - Opened by rebeldroid12 almost 9 years ago
- 8 comments
#15 - Created requirements file for all pip install packages
Pull Request -
State: closed - Opened by rebeldroid12 almost 9 years ago
#14 - Rework the mapping so that it scales to the size of the real datasets
Issue -
State: closed - Opened by mandel01 almost 9 years ago
- 1 comment
Labels: high priority
#13 - Process reads file (.fastq) by demultiplexing
Issue -
State: closed - Opened by mandel01 almost 9 years ago
- 3 comments
Labels: high priority
#12 - disruption fraction (i.e., threePrimeness) is not working
Issue -
State: closed - Opened by mandel01 about 9 years ago
- 1 comment
Labels: bug
#11 - Bundle bowtie directly in the package
Issue -
State: closed - Opened by mandel01 about 9 years ago
- 2 comments
Labels: enhancement
#10 - Documentation
Issue -
State: closed - Opened by biobenkj about 9 years ago
- 2 comments
Labels: help wanted
#9 - License
Issue -
State: closed - Opened by biobenkj about 9 years ago
- 2 comments
Labels: lower priority
#8 - Overall optimization
Issue -
State: closed - Opened by mandel01 about 9 years ago
- 7 comments
Labels: enhancement
#7 - Summary of results and logging
Issue -
State: closed - Opened by mandel01 about 9 years ago
- 12 comments
#6 - `filterSortCounts()` sorting as strings
Issue -
State: closed - Opened by mandel01 about 9 years ago
- 1 comment
Labels: lower priority
#5 - Barcodes are not being filtered out properly
Issue -
State: closed - Opened by mandel01 about 9 years ago
- 1 comment
Labels: bug
#4 - CPM are binning at 10/100/1000
Issue -
State: closed - Opened by mandel01 about 9 years ago
- 4 comments
#3 - Code testing and test datasets
Issue -
State: closed - Opened by biobenkj about 9 years ago
- 3 comments
#2 - Excel-generated tsv files don't work for demultiplex.py
Issue -
State: closed - Opened by mandel01 over 9 years ago
- 2 comments
Labels: bug
#1 - Images for README.md
Issue -
State: closed - Opened by mandel01 over 9 years ago