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

#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

#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