lpantano/DEGreport

Issues

• Connecting dots and lines in degPlotCluster()

  #66 opened 2 months ago by CroixJeremy2
  1

• degCovariates does not shade by r value

  #58 opened 4 months ago by hwick
  5

• Plot shows only one coldata group on x-axis

  #42 opened 4 months ago by elcega
  3

• Problem with `summarise()`

  #37 opened 4 months ago by Bithorax
  4

• issues with degPatterns not setting Time in Normalize

  #57 opened 4 months ago by kesner
  8

• `lasso2` dependency no longer on CRAN

  #53 opened 4 months ago by kennyworkman
  5

• Regarding Group # from degPatterns Output

  #51 opened 4 months ago by drives28
  2

• Regarding Clustering Based on Expression Pattern

  #52 opened 4 months ago by drives28
  1

• Validate the clusters from degPatterns

  #49 opened 4 months ago by lgallegovillar
  2

• Extract One Cluster Plot from degPlotCluster

  #46 opened 4 months ago by drives28
  3

• Show Expression Changes from One Cluster

  #45 opened 4 months ago by drives28
  5

• Extract the genes of each group pattern

  #41 opened 4 months ago by elcega
  3

• Extracting Gene-Gene distance matrix from DegPatterns

  #47 opened 4 months ago by chk63
  3

• degPatterns error

  #27 opened 4 months ago by wangmhan
  8

• Error in DEGpatterns: could not find function "set"

  #60 opened 4 months ago by gowgowuk
  11

• `scale` parameter is missing in `degPCA`

  #63 opened 4 months ago by bounlu
  1

• z-scores of gene abudance

  #44 opened 4 months ago by RubenRBakker
  10

• Boxplot position

  #55 opened 4 months ago by Chunhuixu
  1

• How does degPatterns() decide what height to use for cutting tree

  #59 opened 4 months ago by sang-15
  1

• New genes that did not exist in dds object suddenly showed up after degPatterns

  #65 opened 7 months ago by sandray-imp
  1

• Clarification with degMerge function

  #64 opened 7 months ago by Chengyao-Peng
  1

• degPatterns crashes because of stack overloading

  #62 opened 6 months ago by NastiaSkuba
  9

• lasso2 is an R4 only package

  #43 opened 7 months ago by alpapan
  1

• Sort each cluster graph numerically

  #48 opened 3 years ago by bacas2
  1

• Error in rep("one_group", nrow(metadata)) : invalid 'times' argument

  #39 opened 4 years ago by elcega
  8

• Error in install.packages : ERROR: failed to lock directory

  #40 opened 4 years ago by venuraherath
  1

• `degCovariates`: breaking change in dplyr filter code

  #36 opened 4 years ago by mjsteinbaugh
  6

• How to re-cluster in each group for DEGpattern?

  #35 opened 4 years ago by ShaowenJ
  0

• Wrong clusters identification

  #34 opened 4 years ago by jgarces02
  2

• Can we order the top N genes within degplot

  #33 opened 4 years ago by klai001
  5

• degCovariates ERROR

  #32 opened 5 years ago by algilm
  1

• How is variance explained calculated for degCovariates?

  #31 opened 5 years ago by Zepeng-Mu
  2

• error message

  #30 opened 5 years ago by NextGenBioinformatics
  1

• Add prefix to the title plot

  #29 opened 5 years ago by lpantano
  0

• degPatterns results exists unsimilar pattern in a cluster

  #28 opened 5 years ago by etbuface
  1

• Incorrect reordering of TimeSeries in degPattern

  #26 opened 5 years ago by sum732
  2

• bug in degPlotWide() (v. 1.18.1) only works if group="group"

  #25 opened 6 years ago by hexaflexa
  2

• degCheckFactors error

  #23 opened 6 years ago by maria-xi
  4

• Check class

  #21 opened 7 years ago by lpantano
  0

• Adapt plots to handle DEGSet class

  #19 opened 7 years ago by lpantano
  0

• Adapt DEGSet to limma output

  #20 opened 7 years ago by lpantano
  0

• Clean data to use in example

  #15 opened 7 years ago by lpantano
  0

• move NEWS to parent directory

  #17 opened 7 years ago by lpantano
  0

• Add method to get data.frame table

  #18 opened 7 years ago by lpantano
  0

• Add DEGresults examples to vignette

  #16 opened 7 years ago by lpantano
  0

• Migrate to testthat

  #14 opened 7 years ago by lpantano
  0

• NAMESPACE with roxygen2

  #12 opened 7 years ago by lpantano
  0

• add pvalue to degCovariates

  #10 opened 7 years ago by lpantano
  0

• degPCA to have only ma as input

  #11 opened 7 years ago by lpantano
  0

• add function for PCA vs metadata correlation

  #9 opened 7 years ago by lpantano
  1