Danko-Lab/BayesPrism

Issues

• Cell state co-occurrence analysis

  #99 opened 3 months ago by ConDem94
  1

• BayesPrism on microarray data

  #98 opened 3 months ago by ConDem94
  0

• I am unable to successfully install this R package

  #97 opened 3 months ago by ksdonaldduck
  2

• Can I used BayesPrism to perform deconvolution on the microarray results by the scRNAseq reference

  #96 opened 3 months ago by ZhijieHanbioinfor
  2

• Question about calculate the immune cell fraction in bulk sequencing of tumor sample

  #95 opened 3 months ago by threshold233
  2

• Re-input the result into the seurat object

  #94 opened 4 months ago by JaneeeeeeW
  1

• Deconvolution Using BayesPrism for Tumor Subtypes

  #88 opened 4 months ago by xianjieshen
  2

• Final Theta of cell state

  #82 opened 7 months ago by RoyEHanna
  3

• why cell type specific gene expression inference is so much better for cancer cells than for the rest ?

  #93 opened 4 months ago by Sophon-0
  1

• Question and suggestion for running with large bulk sample set

  #92 opened 5 months ago by FGOSeal
  1

• sc.dat is single cell or bulk seq matrix?

  #62 opened 5 months ago by trusha0911
  3

• Using known cell type fractions

  #90 opened 5 months ago by oriolpich
  2

• Example about Computing z-scores of signature genes for Z of the cell type of interest.

  #85 opened 5 months ago by 1667857557
  3

• Using selected cell type markers can't improve the accuracy

  #91 opened 5 months ago by sherry1000001
  0

• Mouse or human (?) for option "species"

  #89 opened 5 months ago by yingzhang121
  1

• Discrepancies Between matched Single-cell and Bulk Transcriptome Samples

  #86 opened 6 months ago by Rui-Jing
  1

• gene names of reference and mixture do not match!

  #87 opened 6 months ago by rmontagn
  1

• cell type correlation in the reference

  #81 opened 6 months ago by youcef-benmohammed
  0

• How much memory consumed per core?

  #84 opened 7 months ago by Pentayouth
  1

• I just want to quantify the various cell types within T cells, is this feasible?

  #83 opened 7 months ago by M-jk22
  1

• reference single cell

  #80 opened 8 months ago by youcef-benmohammed
  1

• optimal number of each cell state

  #79 opened 8 months ago by inofechm
  3

• Issue with run.prism Function

  #73 opened a year ago by Hananebh
  2

• installation error

  #78 opened 9 months ago by Mjaraespejo
  0

• use sparse matrices instead of full matrices ?

  #58 opened a year ago by rmontagn
  4

• library size normalization of inferred counts?

  #77 opened 10 months ago by vravik
  1

• Can BayesPrism be used to deconvolute normal and disease muscle tissues to different cell types?

  #76 opened 10 months ago by guodudou2
  2

• imput of Bulk RNA-seq have negative after romoving batch effect

  #75 opened a year ago by Lily159753
  1

• question

  #69 opened a year ago by iwanttoeatyo
  1

• Using Bayes Prism in Python

  #74 opened a year ago by jw235
  0

• cell state label is mandatory ?

  #66 opened a year ago by martina811
  2

• Issue with BayesPrism Gateway

  #72 opened a year ago by soph1azhao
  1

• Deconvolved estimates matching known cell type proportions

  #67 opened a year ago by njrobins
  2

• Less genes in cell-specific gene expression count matrix Z

  #71 opened a year ago by WuRAFY
  0

• Low lymphocyte fraction in lung adenocarcinoma

  #57 opened a year ago by WuRAFY
  7

• Do we need to merge our expression file (RNA-seq) and our reference file (scRNA-seq) as our input file?

  #70 opened a year ago by misha832
  1

• Z expression matrix

  #68 opened a year ago by martina811
  7

• Principle of separation of types?

  #65 opened a year ago by Lao-Tz
  8

• get.fraction function can not extract the deconvolution information for state

  #63 opened a year ago by Lao-Tz
  2

• Error in validObject(.Object) : invalid class “prism” object: invalid key

  #64 opened a year ago by faenee
  0

• Is the function: get.exp.stat() using p.value or FDR as default

  #61 opened a year ago by Aeget1000
  0

• Error: if (any(which.row)) { : missing value where TRUE/FALSE needed

  #60 opened a year ago by pcr08
  4

• Deconvolution with tissues as cell states and annotated cell labels as cell types

  #59 opened a year ago by FedericoVann
  2

• Reference with Integrated Matrices Containing Negative Values

  #56 opened a year ago by FedericoVann
  2

• Fail to install package

  #55 opened a year ago by KaWingLee9
  2

• Expression contribution of different cell types to a gene

  #52 opened a year ago by WuRAFY
  3

• Differential Expression and GSEA

  #51 opened a year ago by emilylasse
  3

• Similar error while running `plot.cor.phi` and `plot.scRNA.outlier` functions ('x' must be an array of at least two dimensions)

  #49 opened a year ago by iamakhilverma
  2

• Error in get.exp.stat

  #50 opened a year ago by wlei-amu
  6

• Installation problem with error message ‘Matrix (>= 1.5.0)’ is not available

  #48 opened a year ago by alexdray86
  1