Code

Import commit history from slam_3UIs#46

Code

Merged

ns-rse merged 63 commits intomainsudlab/IsoSLAM:mainfrom ns-rse/31-import-slam_3UIssudlab/IsoSLAM:ns-rse/31-import-slam_3UIsCopy head branch name to clipboardNov 20, 2024

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Commits

Commits on Aug 29, 2023

• initial commit before ian started messing with it

  IanSudbery

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Commits on Jan 23, 2024

• first commit

  jjriley1

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• following receipt of seq data

  jjriley1

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• Fixed errors re salmon index and quant

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Commits on Feb 7, 2024

• Added script to assign reads to spliced and unspliced isoform, and get metadata for each read.

  jjriley1

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• Updated comments.

  jjriley1

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• Changed RI assignment to only look at JC, and only focus on 3' junction

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Commits on Feb 9, 2024

• Updated 3UI info call to use bed6 not default bed

  jjriley1

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• updated retained read assignment to use exon counts. add chr and strand to output

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Commits on Mar 12, 2024

• Added dapars scripts and config for gene level APA across diff

  

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• Added scripts and pipeline method to get pval for difference between splice pairs

  

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• Added script to get pval for differences in each isoform over differentiation time

  

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• Added script to get pval for gene level stability differences over diff time

  

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• Script to assign reads at gene level

  

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• Script to get pvals for differences in isoform ratios over time

  

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• Pipeline updated to do gene level analysis, and get pvals for between_pair, across_time, and interaction

  

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Commits on Jun 28, 2024

• updated pipeline and config

  jjriley1

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• updated following code review with IS

  jjriley1

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• updated following code review with IS pt2

  jjriley1

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• script to do conversions for all introns, not just 3utr, and output

  jjriley1

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• script to summarize pct_converted instead of doing in each script

  jjriley1

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• script to do decay curves and pvals for all introns not just 3utr

  jjriley1

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Commits on Oct 31, 2024

• Move text from README.txt > README.md

  ns-rse

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• Merge pull request #2 from jjriley1/ns-rse/demo

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• Test to see how branch switching works

  JackJRiley

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• Removed unnecessary pipeline functions and corresponding scripts

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• Added script description

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• Removed non-accessed imports

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Commits on Nov 1, 2024

• chore: info added to README.md; tidying Python code

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• Merge pull request #3 from jjriley1/ns-rse/tidying-20241101

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Commits on Nov 11, 2024

• Changed hardcoded input files to test set

  JackJRiley

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• Merge branch 'jjriley1/1-tidy-up' of github.com:jjriley1/slam_3UIs into jjriley1/1-tidy-up

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• removed blank lines

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Commits on Nov 14, 2024

• refactor: Switching to f-strings and removing CamelCase

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Commits on Nov 15, 2024

• Initial commit

  ns-rse

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• ci: Workflow to add issues to project automatically

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• chore: Ignore PyChrm,VSCode,Emacs,OSX files

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• chore: Adds CODE_OF_CONDUCT.md

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• chore: Adds MIT License and CITATION.cff

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• doc: First draft of README

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• Fix error in badges of README.md

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• Adding missing line to header of README.md

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• packaging: Adds initial pyproject.toml

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• chore: Adding bug report and feature request issue templates

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• bug(issuetemplates): Fixing issues in issue templates

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• bug(issuetemplate): Another attempt at fixing Bug Report template

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• docs(readthedocs): Adds configuration file for readthedocs

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• package: Initial dependencies added to pyproject.toml

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• ci(pre-commit): Adding pre-commit, markdownlint-cli2 & pylint conf

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• style: Linting existing files with pre-commit hooks

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• docs: Setting up Sphinx documentation

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• ci: Adding multiversionopts

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• ci/docs: Move sphinx conf.py to work with CI; tweak sphinx workflow

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• ci: remove run from step

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• ci: Move docs/conf.py > docs/source/conf.py

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• ci: add explicit config file option for sphinx-multiversion

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• ci: correct path to conf.py in .readthedocs.yaml

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• ci: restrict tmate to only run if there is a failure

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• admin: Links to contributing from README.md

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• build: minimal set of dependencies

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• ci: Add workflow for testing action

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• feature: Initial import of basic pipeline from jjriley1/slam_3UIs

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Commits on Nov 20, 2024

• Merge branch 'main' into ns-rse/31-import-slam_3UIs

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