Ecosyste.ms: Issues

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GitHub / miraep8/rendseq issues and pull requests

#64 - Update tests for make wig

Pull Request - State: closed - Opened by miraep8 about 1 year ago

#63 - Adding end to end and adding tests for make wig

Pull Request - State: closed - Opened by miraep8 about 1 year ago - 2 comments

#62 - Fix CI/CD tests

Pull Request - State: closed - Opened by miraep8 about 1 year ago - 1 comment

#61 - Updating Documentation

Pull Request - State: closed - Opened by miraep8 about 1 year ago - 2 comments

#60 - Fix zscore tests

Pull Request - State: closed - Opened by miraep8 about 1 year ago

#58 - Add raw reads/peak based shadow removal

Issue - State: open - Opened by miraep8 over 1 year ago

#56 - Version 0.1.9

Pull Request - State: closed - Opened by miraep8 over 1 year ago

#55 - Increase speed of z score calcuations

Pull Request - State: closed - Opened by miraep8 over 1 year ago - 1 comment

#54 - quick bump version

Pull Request - State: closed - Opened by miraep8 over 1 year ago

#53 - Fix the z score tests

Issue - State: closed - Opened by miraep8 over 1 year ago - 1 comment

#52 - Fixing Padding and Speeding up Z score calling

Pull Request - State: closed - Opened by miraep8 over 1 year ago - 1 comment

#51 - Release 0.1.6

Pull Request - State: closed - Opened by miraep8 over 1 year ago

#50 - Removes CLI interface support in zscores and make_peaks

Pull Request - State: open - Opened by miraep8 over 1 year ago - 1 comment

#49 - Cleanup + Bug fixes in z_scores module.

Pull Request - State: closed - Opened by miraep8 over 1 year ago - 2 comments

#48 - Creating the yaml file for the release

Pull Request - State: closed - Opened by miraep8 over 1 year ago

#47 - Maitenence - bumping isort hook version

Pull Request - State: closed - Opened by miraep8 over 1 year ago - 1 comment

#46 - Pipeline sometimes fails to call obvious peaks if one side has very few reads!

Issue - State: closed - Opened by miraep8 over 1 year ago
Labels: bug

#45 - Add notebooks to readthedocs

Issue - State: open - Opened by julianstanley over 2 years ago - 2 comments
Labels: documentation, good first issue

#44 - Add a parameter to name kink image in thresh_peaks

Pull Request - State: open - Opened by julianstanley over 2 years ago - 4 comments

#43 - Ramp calling module

Pull Request - State: closed - Opened by conniesaur over 2 years ago - 3 comments

#42 - Implement a web interface

Issue - State: open - Opened by julianstanley over 2 years ago - 4 comments
Labels: enhancement, brainstorming/planning

#41 - Remove Command Line Interface

Issue - State: closed - Opened by miraep8 over 2 years ago - 2 comments

#40 - Identify and remove PCR jackpots

Issue - State: open - Opened by julianstanley over 2 years ago - 9 comments
Labels: enhancement, brainstorming/planning

#39 - Add functionality for relevant biological questions

Issue - State: open - Opened by miraep8 over 2 years ago
Labels: brainstorming/planning

#38 - Create a github action to automate pypi release

Issue - State: open - Opened by miraep8 over 2 years ago
Labels: maintenance

#37 - store data in objects rather than arrays?

Issue - State: open - Opened by miraep8 over 2 years ago - 1 comment
Labels: enhancement, question, brainstorming/planning

#36 - jupyter notebook for basic rendseq tutorial

Pull Request - State: closed - Opened by miraep8 over 2 years ago - 2 comments

#35 - Throw error if HMM peaks can not be computed.

Pull Request - State: closed - Opened by miraep8 over 2 years ago - 5 comments

#34 - Lets Squash our merges?

Issue - State: closed - Opened by miraep8 over 2 years ago - 5 comments
Labels: maintenance

#33 - Quick README typo fixes

Pull Request - State: closed - Opened by julianstanley over 2 years ago - 2 comments

#32 - Figure out where to host documentation!

Issue - State: closed - Opened by miraep8 over 2 years ago - 5 comments
Labels: documentation, maintenance

#31 - Added a basic sphinx doc site + some readme updates

Pull Request - State: closed - Opened by julianstanley over 2 years ago - 12 comments

#30 - Just a quick test for #29 and #12

Pull Request - State: closed - Opened by julianstanley over 2 years ago - 5 comments

#29 - trim z scores before hmm peaks

Pull Request - State: closed - Opened by miraep8 over 2 years ago - 3 comments

#28 - Add more tests for hmm_peaks

Issue - State: open - Opened by miraep8 over 2 years ago
Labels: maintenance

#27 - adding PR template, making some changes to the .gitignore

Pull Request - State: closed - Opened by miraep8 over 2 years ago

#26 - Add pytests to CI

Pull Request - State: closed - Opened by miraep8 over 2 years ago - 5 comments

#25 - Adding CI tests for pytests

Pull Request - State: closed - Opened by miraep8 over 2 years ago

#24 - Trilom doesn't allow CI testing on windows

Issue - State: closed - Opened by julianstanley over 2 years ago - 2 comments
Labels: maintenance

#23 - Add multiple OSs to workflow

Pull Request - State: closed - Opened by julianstanley over 2 years ago - 3 comments

#22 - Refactor file paths

Issue - State: open - Opened by julianstanley over 2 years ago
Labels: help wanted, good first issue, maintenance

#21 - fixing the pytest file not found error on windows

Pull Request - State: closed - Opened by miraep8 over 2 years ago - 1 comment

#20 - local pytest run seems to have issues?

Issue - State: closed - Opened by miraep8 over 2 years ago - 2 comments
Labels: bug

#19 - Should parsing functions go into file_funcs?

Issue - State: open - Opened by julianstanley over 2 years ago
Labels: good first issue, maintenance

#18 - Put in more checks for correct argument type

Issue - State: open - Opened by miraep8 over 2 years ago
Labels: good first issue, maintenance

#17 - Create a PR template.

Issue - State: closed - Opened by miraep8 over 2 years ago
Labels: maintenance

#16 - Adding CI, made style changes

Pull Request - State: closed - Opened by miraep8 over 2 years ago - 3 comments

#15 - Add logging functionality

Issue - State: open - Opened by miraep8 over 2 years ago - 1 comment
Labels: maintenance

#14 - Testing suite and associated refactoring

Pull Request - State: closed - Opened by julianstanley over 2 years ago - 4 comments

#13 - p_to_p = 1 doesn't stay in peak state

Issue - State: closed - Opened by julianstanley over 2 years ago - 3 comments
Labels: bug

#12 - hmm_peaks can't detect very extreme peaks

Issue - State: closed - Opened by julianstanley over 2 years ago - 2 comments
Labels: bug

#11 - Vectorized populate_trans_mat

Pull Request - State: closed - Opened by conniesaur over 2 years ago - 3 comments

#10 - What is the Z-score of a point with invalid left and right Z-scores?

Issue - State: closed - Opened by julianstanley over 2 years ago - 5 comments

#9 - Adapt to bedgraph or multi-chromosome wig

Issue - State: open - Opened by julianstanley over 2 years ago - 1 comment
Labels: enhancement

#8 - Should file_funcs take a file handle instead?

Issue - State: closed - Opened by julianstanley over 2 years ago - 2 comments

#7 - Vectorize functions

Issue - State: closed - Opened by conniesaur over 2 years ago - 1 comment

#6 - Add codecov

Issue - State: closed - Opened by julianstanley over 2 years ago - 5 comments
Labels: maintenance

#5 - Add continuous integration

Issue - State: closed - Opened by julianstanley over 2 years ago - 7 comments
Labels: maintenance

#4 - Add more optional arguments to command line interface for make_peaks

Issue - State: open - Opened by miraep8 over 2 years ago
Labels: enhancement, good first issue

#3 - Create a tutorial!

Issue - State: closed - Opened by miraep8 over 2 years ago - 1 comment
Labels: documentation

#2 - Add some basic test cases

Issue - State: closed - Opened by miraep8 over 2 years ago - 3 comments
Labels: enhancement, testing

#1 - [Planning] - What type of generative model should we implement?

Issue - State: open - Opened by miraep8 over 2 years ago - 1 comment
Labels: enhancement, testing, brainstorming/planning