thelovelab/DESeq2

Issues

• DESeqDataSet() fails when the count matrix contains a value higher than .Machine$integer.max

  #66 opened 2 months ago by frederikziebell
  9

• Pseudogenes with covariates

  #104 opened 2 months ago by OlgaVT
  1

• What defines a gene as "low counts [2]"

  #103 opened 3 months ago by jamespblloyd-uwa
  1

• DESeq2 Vignette: Issue with pheatmap clustering distance measure

  #102 opened 3 months ago by SuhasSrinivasan
  1

• The log2FC is not match with average of normalized raw counts values

  #101 opened 4 months ago by lida-R
  1

• Is it possible to apply Differential isoform Expression

  #100 opened 4 months ago by Tang-pro
  1

• How can I install DESeq2 with Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 (2024-04-24)

  #99 opened 5 months ago by monis4567
  1

• A question about whether to add 1 to the raw count before Deseq2 analysis

  #98 opened 5 months ago by jessicaliu09
  1

• Cook's distance discrepancy between Wald and LRT

  #97 opened 5 months ago by rasmushenningsson
  4

• limma::removeBatchEffect section of tutorial not working properly?

  #94 opened 7 months ago by andrebolerbarros
  3

• Add possibility to simulate data

  #90 opened 7 months ago by frederikziebell
  2

• how to get a gtf file when using tximprot for an organism without genome sequence and annotation file

  #93 opened 7 months ago by luwd401
  1

• How to export the normalized matrix of RNA-seq?

  #92 opened 8 months ago by hyjforesight
  2

• the model matrix is not full rank issue

  #91 opened 9 months ago by Guangsheng357
  0

• DESeq2 Summarized Experiment Unable to Install

  #89 opened 10 months ago by emgreen1014
  1

• DESeq2 for single-cell pseudobulk: top genes have low expression

  #88 opened 10 months ago by DaianeH
  2

• save of DESeq2::DESeqDataSet

  #87 opened a year ago by christophista
  6

• collapseReplicates() bug / bad behavior

  #86 opened a year ago by mikelove
  0

• results.R help

  #85 opened a year ago by biounix
  1

• Figure of plotMA

  #83 opened a year ago by yueli8
  2

• import MatrixGenerics

  #82 opened a year ago by waddella
  2

• DESEq2 error

  #80 opened a year ago by imrjesh
  1

• Installation error:

  #81 opened a year ago by desmodus1984
  1

• How did you decide the default significance level to be 0.1 in results()?

  #79 opened a year ago by hchoiHiLung
  1

• Parallelization bug on DESEq2 v 1.40.1

  #75 opened a year ago by BenjaminDEMAILLE
  6

• a slight generalization of plotPCA made at CSAMA 23

  #78 opened a year ago by vjcitn
  0

• error in saving up and down regulated genes

  #77 opened a year ago by SREESHMARAJ659
  5

• lfcShrink -> Error in optimHess

  #74 opened a year ago by mikelove
  1

• Significance testing with multi-condition single cell data: LRT, Wald test, or both?

  #76 opened a year ago by mariecrane
  6

• glmGamPoi with LRT then lfcShrink

  #73 opened a year ago by mikelove
  1

• DESeqDataSetFromMatrix error

  #69 opened a year ago by abhijitcbio
  1

• Unexpected behaviour from results(contrast) argument

  #72 opened a year ago by JCSzamosi
  2

• lfcShrink error

  #71 opened a year ago by mmparedes5
  2

• issue with installing the package on Apple M1 Max

  #70 opened a year ago by sophieastrof
  2

• Normalization of RNA seq data before DESeq2

  #68 opened 2 years ago by Mercilena
  1

• Updating version introduced optim error with apeglm

  #67 opened 2 years ago by JCSzamosi
  1

• Potential problem with independent filtering

  #65 opened 2 years ago by s-a-nersisyan
  1

• MeanSD plot

  #60 opened 2 years ago by L3ft2di3
  14

• svalue argument seems not work in lfcShrink

  #62 opened 2 years ago by z5ouyang
  4

• Archive 'many samples' tweetorial

  #61 opened 2 years ago by frederikziebell
  2

• How to plot PCA without background grid lines?

  #57 opened 2 years ago by mathavanpu
  1

• Parallel processing broken in R4.2

  #50 opened 2 years ago by frederikziebell
  3

• vst blind

  #56 opened 2 years ago by igordot
  2

• Add testing against a threshold for ashr shrinkage

  #53 opened 2 years ago by frederikziebell
  7

• Different DESeq2 results (both FC and pvalue) by changing col/row orders in input

  #55 opened 2 years ago by weishwu
  1

• About normalized counts of DESeq2

  #54 opened 2 years ago by gouwei1
  1

• Can DESeq2 deal with comparison between different species?

  #52 opened 2 years ago by gouwei1
  6

• weired dispersion and mean

  #51 opened 2 years ago by wangjiawen2013
  1

• Unable to import data when using single factor

  #49 opened 3 years ago by pati-ni
  3

• How to get DESeq2 results in large count matix files?

  #48 opened 3 years ago by mathavanpu
  2