Issues

• AnnotationHub returns poor results in lcdbwf

  lcdb/lcdb-wf#432 · Filter by author njohnso6 opened on Feb 28, 2025

• Configure functional enrichment to work with GSEA

  lcdb/lcdb-wf#424 · Filter by author b-full opened on Dec 13, 2024

• FDR cutoff alpha not applied in rnaseq.Rmd

  lcdb/lcdb-wf#422 · Filter by author Mira0507 opened on Dec 3, 2024

• use fasterq-dump

  lcdb/lcdb-wf#409 · Filter by author daler opened on Oct 8, 2024

• SRA runs should save data elsewhere and then symlink

  lcdb/lcdb-wf#408 · Filter by author daler opened on Oct 8, 2024

• Layout rather than LibraryLayout

  lcdb/lcdb-wf#407 · Filter by author daler opened on Oct 8, 2024
  2

• Add hyperlink to rnaseq.Rmd error message, 'duplicate names found after removing pattern ^contr_[^_]+_'

  lcdb/lcdb-wf#395 · Filter by author menoldmt opened on Nov 28, 2023
  1

• In functional-enrichment.Rmd and gene-patterns.Rmd, add config for turning on/off lazy caching

  lcdb/lcdb-wf#391 · Filter by author menoldmt opened on Aug 16, 2023
  1

• Automatic plot resizing in gene-patterns

  lcdb/lcdb-wf#390 · Filter by author menoldmt opened on Aug 16, 2023

• Add Functional Enrichment TSV Links to functional-enrichment.Rmd

  lcdb/lcdb-wf#389 · Filter by author menoldmt opened on Aug 16, 2023
  1

• Typographical errors in Gene-Patterns Explanatory Text

  lcdb/lcdb-wf#388 · Filter by author menoldmt opened on Aug 16, 2023

• In gene-patterns.Rmd, ensure factors for certain colData used in gene patterns

  lcdb/lcdb-wf#387 · Filter by author menoldmt opened on Aug 16, 2023

• PDF plots in gene-patterns.Rmd

  lcdb/lcdb-wf#386 · Filter by author menoldmt opened on Aug 16, 2023

• consider using black/greylists for peak-calling

  lcdb/lcdb-wf#381 · Filter by author daler opened on Jul 17, 2023

• Document reference configs

  docs
  lcdb/lcdb-wf#355 · Filter by author kcampbell824 opened on Jan 10, 2022
  

• proposal to reorganize output directories

  lcdb/lcdb-wf#352 · Filter by author daler opened on Oct 13, 2021

• Catch "Valid Key Exception" in Functional Enrichment

  lcdb/lcdb-wf#349 · Filter by author fridells51 opened on Oct 1, 2021

• macs2 rule should handle PE better

  lcdb/lcdb-wf#345 · Filter by author daler opened on Sep 3, 2021

• convert circleci tests to more easily run locally

  v1.10
  lcdb/lcdb-wf#344 · Filter by author daler opened on Aug 24, 2021
  1

• preflight reporting

  lcdb/lcdb-wf#343 · Filter by author daler opened on Aug 22, 2021

• rm libsize table and rule

  v1.10
  lcdb/lcdb-wf#342 · Filter by author daler opened on Aug 22, 2021

• fastq-dump arguments

  lcdb/lcdb-wf#328 · Filter by author daler opened on Jan 11, 2021

• Issues with complex dataset

  lcdb/lcdb-wf#310 · Filter by author esnaultc opened on Aug 18, 2020

• update zebrafish reference config

  lcdb/lcdb-wf#296 · Filter by author daler opened on Jun 5, 2020

• Update plotMA.label in helpers

  rnaseq.rmdv1.6
  lcdb/lcdb-wf#292 · Filter by author mitraak opened on May 26, 2020