wejlab/animalcules

Issues

• Unknown "V1" taxa in abundance taxa plot

  #69 opened 4 months ago by IdanBanson
  6

• BIOM file upload brings out error

  #53 opened 10 months ago by IdanBanson
  2

• lazy-load database ... PathoStat.rdb is corrupt

  #50 opened 2 years ago by ReneKat
  3

• No species level option available

  #51 opened 2 years ago by nunrath
  1

• Quick fix for read_pathoscope_data()

  #49 opened 2 years ago by aubreyodom
  1

• Is Alpha rarefaction required?

  #46 opened 3 years ago by s6aamani
  1

• Incorrect options for Select Target Condition in Biomarker Analysis

  #44 opened 3 years ago by jarrodscott
  2

• Counts file - only relative abundance data

  #43 opened 4 years ago by davitero
  2

• Import from phyloseq?

  #38 opened 4 years ago by cjfields
  3

• categorized variables need to be as.character()

  #42 opened 4 years ago by jasonzhao0307
  0

• Adjustable graph size

  #41 opened 4 years ago by Zinthrow
  0

• X11 colors in the barplots area?

  #40 opened 4 years ago by Zinthrow
  0

• Biomarker names cannot handle spaces

  #39 opened 5 years ago by Zinthrow
  2

• linux check error related to Entrez

  #37 opened 5 years ago by jasonzhao0307
  3

• bioc

  #36 opened 5 years ago by jasonzhao0307
  0

• Bioconductor Reviews

  #35 opened 5 years ago by anfederico
  0

• add detail explanation for each button/option in the screen shot

  #34 opened 5 years ago by jasonzhao0307
  4

• Modify tSNE (save the tSNE result to an assay)

  #30 opened 5 years ago by jasonzhao0307
  0

• Complete docs (figures, descriptions, TOC)

  #21 opened 5 years ago by jasonzhao0307
  0

• modify the Boxplot in Abundance

  #26 opened 5 years ago by jasonzhao0307
  0

• add testthat

  #33 opened 5 years ago by jasonzhao0307
  0

• add Limma to Differential abundance analysis using logCPM

  #28 opened 5 years ago by jasonzhao0307
  0

• Modify differential abundance analysis

  #29 opened 5 years ago by jasonzhao0307
  1

• Add a new assay dashboard sub-tab in the "Summary and Filter" tab

  #24 opened 5 years ago by jasonzhao0307
  0

• Add one or two more example datasets and user could select which example dataset to use

  #5 opened 5 years ago by jasonzhao0307
  0

• Add species level to animalcules

  #25 opened 5 years ago by jasonzhao0307
  0

• Microbe filter modify

  #23 opened 5 years ago by jasonzhao0307
  0

• Check/Fix summary statistics

  #22 opened 5 years ago by jasonzhao0307
  0

• Alpha diversity plot continuous dot plot

  #31 opened 5 years ago by jasonzhao0307
  1

• logCPM set to default assay for PCA

  #27 opened 5 years ago by jasonzhao0307
  0

• Summary plot below error

  #32 opened 5 years ago by jasonzhao0307
  1

• Output vignette to GitHub-compatible README

  #18 opened 5 years ago by anfederico
  0

• resolve biocCheck warnings and notes

  #19 opened 5 years ago by jasonzhao0307
  0

• Add more distance metrics for PCoA

  #20 opened 6 years ago by anfederico
  0

• package size NOTE

  #17 opened 6 years ago by jasonzhao0307
  0

• add a logo

  #15 opened 6 years ago by jasonzhao0307
  1

• Fix the building errors

  #14 opened 6 years ago by jasonzhao0307
  0

• Fix devtools:check() run time too long issue

  #16 opened 6 years ago by jasonzhao0307
  5

• Make the Mann Whitney test name consistent for the stat result table name

  #10 opened 6 years ago by jasonzhao0307
  0

• Check all figures, make sure the y-axis and x-axis name makes sense to users

  #12 opened 6 years ago by jasonzhao0307
  0

• Make default tax level being phylum

  #7 opened 6 years ago by jasonzhao0307
  0

• Add a ROC plot to biomarker page

  #9 opened 6 years ago by jasonzhao0307
  0

• modify DE

  #13 opened 6 years ago by jasonzhao0307
  0

• Make each page as simple as possible

  #6 opened 6 years ago by jasonzhao0307
  0

• Add t-SNE and Umap to dim reduction page

  #8 opened 6 years ago by jasonzhao0307
  0

• Change the PCoA 1st and 2nd option name to principle coordinate instead of principle components

  #11 opened 6 years ago by jasonzhao0307
  0