ggloor/ALDEx_bioc

Issues

• Error in var(x) : is.atomic(y) is not TRUE

  #76 opened 25 days ago by Liviacmg
  5

• pairwise T-test always set to FALSE in `aldex()` function

  #75 opened 4 months ago by Yixuan39
  0

• Feature request: implement robust regression in glm to minimizes the influence of outliers

  #74 opened 5 months ago by aimirza
  0

• Feature Request: Support for Using Features/Taxa/Genes as Explanatory Variables in aldex.glm

  #73 opened 5 months ago by aimirza
  0

• How to perform pairwise comparisons between three or more groups in R

  #58 opened a year ago by LeandroD94
  5

• Error when running run_aldex with kruskal or glm_anova for more than 2 level comparisons on "microbiomeMarker" package

  #72 opened 6 months ago by LauGuaUuu
  0

• Adding Scale Uncertainty Fails

  #71 opened 8 months ago by DrLMee
  1

• Rearranging dataframe changes output and Benjamini-Hochberg corrected p-value estimates differ between Bioconductor and developer version

  #70 opened 8 months ago by wiederkf
  0

• Asymmetric datasets

  #69 opened 9 months ago by vyom84
  0

• Cannot install

  #68 opened 9 months ago by theo-allnutt-bioinformatics
  2

• ALDEx2 new version (1.32.0) output effect size difference from (1.28.1)

  #67 opened a year ago by davis-rudolfs
  2

• aldex.ttest not working as demonstrated

  #61 opened a year ago by slschnorr
  1

• Aldex.clr object subsetting description

  #30 opened 4 years ago by K-Pimentel
  2

• Question regarding the significance of the results

  #56 opened a year ago by vdijckthomas
  7

• ALDEx2 on large dataset gives memory not mapped error

  #55 opened a year ago by Rridley7
  13

• aldex.corr giving unexpected results

  #54 opened a year ago by LunavdL
  2

• alr transformation method?

  #24 opened 4 years ago by aimirza
  12

• ALDEx2 clr coerce.data error

  #20 opened 4 years ago by vmaffei
  6

• Log fold change with 95% confidence intervals

  #50 opened 2 years ago by andrewmaltezthomas
  0

• Mean of p-values in aldex.kw()

  #12 opened 2 years ago by masgra
  1

• Aldex clr_function.R bug when using the glm function

  #29 opened 2 years ago by tbrowne5
  1

• How to interpretate the aldex.glm() output?

  #44 opened 2 years ago by zhq90
  1

• Feature request

  #9 opened 2 years ago by stro0070
  4

• effect size for paired samples

  #40 opened 2 years ago by pooranis
  3

• interpretation of t test conflicting results

  #47 opened 2 years ago by elayton13
  2

• Option for providing self-computed IQLR or CLR?

  #31 opened 3 years ago by jolespin
  2

• Subsetting / pairwise comparisons

  #46 opened 3 years ago by elayton13
  1

• `aldex.effect` returns the same effect for every feature when `CI=T`

  #45 opened 3 years ago by amorris28
  1

• aldex.ttest issue

  #43 opened 3 years ago by dkropp2
  2

• aldex.effect include.sample.summary issue

  #41 opened 3 years ago by JEckenberger
  1

• Effect_value_interpretation

  #39 opened 3 years ago by StefanoCast
  2

• Working with multiple timepoints in aldex.glm( )

  #37 opened 4 years ago by mirpie
  0

• suspicious pattern in results

  #36 opened 4 years ago by sformel
  3

• another question about running on HPC

  #34 opened 4 years ago by sformel
  6

• aldex.ttest for paired testing

  #35 opened 4 years ago by sbslee
  2

• Installation via Anaconda not working on Mac OS and Linux

  #33 opened 4 years ago by sbslee
  8

• how to run ALDEX2 on multicore ?

  #32 opened 4 years ago by MonicaSteffi
  4

• Allow cmultRepl from zCompositions and option not to add 0.5 pseudocount

  #28 opened 4 years ago by aimirza
  1

• aldex.glm with model.matrix

  #23 opened 4 years ago by Maraikep
  1

• Negative num. error when running aldex.effect for alr transformation

  #26 opened 4 years ago by aimirza
  1

• `aldex()` - specifically `aldex.effect()` - fails if `conditions` is a factor

  #25 opened 4 years ago by mikemc
  1

• BiocParallel error in clr_effect.r

  #19 opened 5 years ago by jmmack
  2

• Value reported by aldex.corr

  #16 opened 5 years ago by valscherz
  2

• Calculation of Geometric Mean

  #15 opened 5 years ago by kenscripts
  2

• Feature Request: Support for longitudinal/repeated measures data

  #14 opened 5 years ago by mhibberd
  0

• aldex.corr having unexpected behavior

  #13 opened 6 years ago by valscherz
  3

• Store vignette .bib within package

  #7 opened 6 years ago by tpq
  0

• 'verbose' added a column to results if effect = TRUE

  #8 opened 6 years ago by tpq
  1

• Feature request: indicate which condition is positive vs negative

  #2 opened 6 years ago by jmmack
  1

• aldex.clr requires conds

  #1 opened 6 years ago by jmmack
  2