Issues

• Unit test needed - mapProbesToGenes with mapToNearest = T

  QuackenbushLab/NetworkDataCompanion#71 · Filter by author katehoffshutta opened on Apr 4, 2025

• gencode update

  QuackenbushLab/NetworkDataCompanion#63 · Filter by author katehoffshutta opened on Feb 27, 2025

• vague message in gene ID conversion

  QuackenbushLab/NetworkDataCompanion#62 · Filter by author katehoffshutta opened on Feb 21, 2025
  2

• Add network-based gene set enrichment analysis

  enhancement
  QuackenbushLab/NetworkDataCompanion#59 · Filter by author katehoffshutta opened on Feb 21, 2025

• could not find function "CreateTCGAPurityFilteringObject"

  QuackenbushLab/NetworkDataCompanion#58 · Filter by author katehoffshutta opened on Feb 17, 2025
  1

• logCPM and logTPM are not coherent

  QuackenbushLab/NetworkDataCompanion#48 · Filter by author violafanfani opened on May 10, 2024
  4

  

• Support for ignoring NAs of individual probes in mean promoter methylation computation

  enhancement
  QuackenbushLab/NetworkDataCompanion#40 · Filter by author FischerJoBio opened on Oct 20, 2023
  2

  

• Rds_gene_info with duplicates

  QuackenbushLab/NetworkDataCompanion#34 · Filter by author soelmicheletti opened on Aug 23, 2023

• Gene map ensembl ids are transcripts probeToMeanPromoterMethylation

  QuackenbushLab/NetworkDataCompanion#27 · Filter by author FischerJoBio opened on Jul 26, 2023
  4

• Implement flexible slicing in methylation probe mapping

  enhancement
  QuackenbushLab/NetworkDataCompanion#14 · Filter by author katehoffshutta opened on Dec 6, 2022
  2