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cozygene
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bisque
An R toolkit for estimation of cell composition from bulk expression data
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I found the use of bisqueRNA on microarray data, any comment?
#44
Pentayouth
opened
1 week ago
0
Error in CountsToCPM(bulk.eset) : Zero expression in selected genes for 1 cells
#43
yelly-zhou
opened
1 month ago
0
No overlapping genes between markers and bulk.eset
#42
MobinKhoramjoo
opened
1 month ago
2
SeuratToExpressionSet error with seurat v5
#41
Prathyusha-konda
opened
7 months ago
0
Can I use TCGA's TPM data format for bulk RNA as input to bisque?
#40
suhuanhou
closed
7 months ago
1
Prepare for upcoming Seurat v5 release
#39
saketkc
opened
11 months ago
0
MarkerBasedDecomposition overlapping genes error
#38
nikita-telkar
opened
11 months ago
3
Negative proportion values
#37
ssamberkar
closed
1 year ago
1
Lack of "ground truth"markers and estimation
#36
ssamberkar
closed
1 year ago
1
Error in out[[t]]$coefs : $ operator is invalid for atomic vectors
#35
Li-Rui091
closed
1 year ago
1
Input format
#34
Yuling-Zhao
closed
1 year ago
1
Zero expression in selected genes
#33
PalmaGudiel
closed
2 years ago
4
visualization
#32
chenx9
closed
2 years ago
1
SeuratToExpressionSet
#31
chenx9
closed
2 years ago
3
Microarray data?
#30
Yoshi-MutoLab
closed
2 years ago
1
How to interpreter Bisque result
#29
ConcettaDe4
closed
2 years ago
7
Use FPKM or CPM value of bulk RNA seq as input matrix
#28
bugie19
closed
2 years ago
1
supply signature matrix to reference based deconvolution
#27
PelzKo
opened
3 years ago
0
sim.data average proportions taking into account variation between replicates
#26
emmawwinchester
closed
3 years ago
1
how to prepare single cell input from multiple subjects as an input?
#25
complexgenome
closed
3 years ago
1
Adipose dataset
#24
changwn
closed
3 years ago
1
Bulk already in CPM
#23
iriverog
closed
3 years ago
2
Min number of markers in eset?
#22
sjmonkley
opened
3 years ago
2
leave-one-out cross validation
#21
empiricalbayes
closed
3 years ago
2
Error in Generating single-cell based reference
#20
kanekalla
opened
3 years ago
4
SeuratToExpressionSet is not up to date with latest Seurat version
#19
CyrilLagger
opened
3 years ago
4
Weird results ?
#18
alexdray86
closed
3 years ago
2
Typo in SemisupervisedTransformBulk
#17
empiricalbayes
closed
3 years ago
1
add biocViews keyword to DESCRIPTION
#16
grst
closed
3 years ago
2
Error: Zero genes left for decomposition
#15
ShanSabri
closed
3 years ago
11
Counts input for bulk RNAseq dataset
#14
jdarmitage
closed
4 years ago
1
Vignettes and also general questions
#13
uklejaj
closed
4 years ago
3
BisqueRNA Functions not available for usage
#12
Amandahsr
closed
4 years ago
3
Include covariates for residual CPM
#11
quattro
opened
4 years ago
1
Cannot download raw data
#10
OnlyBelter
closed
4 years ago
2
CountsToCPM after extracting markers
#9
randel
closed
4 years ago
2
check for few marker genes
#8
marcalva
closed
4 years ago
1
Errors in MarkerBasedDecomposition
#7
yuewangpanda
closed
4 years ago
6
Deconvolution for a specific part of bulk tissue RNAseq using scRNAseq data?
#6
hellocita
closed
4 years ago
1
bisque in conda-forge / bioconda
#5
favilaco
closed
5 years ago
2
Bulk deconvolution using public scRNA seq data?
#4
Biomiha
closed
5 years ago
13
Expects normalized expression data
#3
marcalva
closed
5 years ago
0
Updated reference-free functions
#2
marcalva
closed
5 years ago
0
Added PCA-based deconvolution
#1
marcalva
closed
5 years ago
0