cozygene/bisque

Issues

• Error in CountsToCPM(bulk.eset) : Zero expression in selected genes for 1 cells

  #43 opened 6 months ago by JJJelly77
  1

• I found the use of bisqueRNA on microarray data, any comment?

  #44 opened 5 months ago by Pentayouth
  0

• No overlapping genes between markers and bulk.eset

  #42 opened 6 months ago by MobinKhoramjoo
  2

• SeuratToExpressionSet error with seurat v5

  #41 opened a year ago by Prathyusha-konda
  0

• Can I use TCGA's TPM data format for bulk RNA as input to bisque?

  #40 opened a year ago by suhuanhou
  1

• Prepare for upcoming Seurat v5 release

  #39 opened a year ago by saketkc
  0

• MarkerBasedDecomposition overlapping genes error

  #38 opened a year ago by nikita-telkar
  3

• Negative proportion values

  #37 opened 2 years ago by ssamberkar
  1

• Lack of "ground truth"markers and estimation

  #36 opened 2 years ago by ssamberkar
  1

• How to interpreter Bisque result

  #29 opened 3 years ago by ConcettaDe4
  7

• Error in out[[t]]$coefs : $ operator is invalid for atomic vectors

  #35 opened 2 years ago by Li-Rui091
  1

• Input format

  #34 opened 2 years ago by Yuling-Zhao
  1

• Zero expression in selected genes

  #33 opened 2 years ago by PalmaGudiel
  4

• visualization

  #32 opened 2 years ago by chenx9
  1

• SeuratToExpressionSet

  #31 opened 3 years ago by chenx9
  3

• Microarray data?

  #30 opened 3 years ago by Yoshi-MutoLab
  1

• Use FPKM or CPM value of bulk RNA seq as input matrix

  #28 opened 3 years ago by bugie19
  1

• SeuratToExpressionSet is not up to date with latest Seurat version

  #19 opened 4 years ago by CyrilLagger
  4

• Adipose dataset

  #24 opened 3 years ago by changwn
  1

• how to prepare single cell input from multiple subjects as an input?

  #25 opened 3 years ago by complexgenome
  1

• sim.data average proportions taking into account variation between replicates

  #26 opened 3 years ago by emmawwinchester
  1

• Bulk deconvolution using public scRNA seq data?

  #4 opened 6 years ago by Biomiha
  13

• Bulk already in CPM

  #23 opened 4 years ago by iriverog
  2

• Min number of markers in eset?

  #22 opened 4 years ago by sjmonkley
  2

• leave-one-out cross validation

  #21 opened 4 years ago by empiricalbayes
  2

• Error in Generating single-cell based reference

  #20 opened 4 years ago by kanekalla
  4

• Weird results ?

  #18 opened 4 years ago by alexdray86
  2

• Error: Zero genes left for decomposition

  #15 opened 4 years ago by ShanSabri
  11

• Typo in SemisupervisedTransformBulk

  #17 opened 4 years ago by empiricalbayes
  1

• Counts input for bulk RNAseq dataset

  #14 opened 4 years ago by jdarmitage
  1

• Vignettes and also general questions

  #13 opened 4 years ago by uklejaj
  3

• BisqueRNA Functions not available for usage

  #12 opened 5 years ago by Amandahsr
  3

• CountsToCPM after extracting markers

  #9 opened 5 years ago by randel
  2

• Include covariates for residual CPM

  #11 opened 5 years ago by quattro
  1

• Cannot download raw data

  #10 opened 5 years ago by OnlyBelter
  2

• Errors in MarkerBasedDecomposition

  #7 opened 5 years ago by yuewangpanda
  6

• Deconvolution for a specific part of bulk tissue RNAseq using scRNAseq data?

  #6 opened 5 years ago by hellocita
  1

• bisque in conda-forge / bioconda

  #5 opened 6 years ago by favilaco
  2