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DavisLaboratory
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standR
Spatial transcriptomics analyses and decoding in R
https://davislaboratory.github.io/standR/
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`readGeoMx` Input from GeoMx NGS Pipeline
#37
bharatm26
opened
3 days ago
0
Normalization method inquiry
#36
jheonsuh
closed
1 week ago
1
Inquiry about Normalization Process
#35
jheonsuh
opened
1 month ago
1
Differential expression analysis with limma-voom pipeline
#34
orange-3711
closed
1 week ago
1
PrepareSpatialDecon error message
#33
emiliasiukola
opened
2 months ago
1
Using alternative batch correction methods to RUV
#32
Doc-R-J
opened
2 months ago
1
SpatialDecon using readGeoMx
#31
jjoo12
opened
3 months ago
7
Input file for your own experiment
#30
willros
closed
2 months ago
5
Unable to plot PCA (scater incompatibility?)
#29
iddryg
closed
3 months ago
2
readGeoMx error in rowNames
#28
kav-ita
closed
4 months ago
1
standR Workflow for Cancer Transcriptome Atlas (CTA)
#27
ErickMUO
opened
5 months ago
2
Error in prepareSpatialDecon(spe_tmm) : could not find function "prepareSpatialDecon"
#26
ZoeGerber
closed
3 months ago
1
Update README.md, add citation
#25
ningbioinfo
closed
7 months ago
0
spatialdecon
#24
OnkarMulay
closed
5 months ago
1
issue with prepareSpatialDecon() function
#23
sciotlos
closed
5 months ago
2
add n_assay argument for findBestK
#22
samleenz
opened
9 months ago
0
Rationale for TPM and RPKM
#21
ChelseaCHENX
closed
8 months ago
1
`norm.factors` not being transferred from `SpatialExperiment` to `DGEList`
#20
jaredmcollette
closed
10 months ago
1
readGeoMx error invalid 'row.names' length
#19
RLau0
closed
1 year ago
1
Error in readGeoMx qith rmNegProbe = FALSE
#18
Sigmatilde
closed
10 months ago
1
plotRLExpr() looking for region annotation
#17
Sigmatilde
closed
1 year ago
1
Error in readGeoMx
#16
knadia07
closed
8 months ago
8
bug fix: plotting bugs and preparedecon bug
#15
ningbioinfo
closed
1 year ago
0
removebatcheffect removal and normalization
#14
dksenthil
closed
10 months ago
1
plotScreePCA and plotPCAbiplot with reducedDim
#13
joonlee3
closed
10 months ago
1
Extract normalized expression matrix
#12
GeremyClair
closed
1 year ago
2
add propeller-related function, link it to the deconvolution output.
#11
ningbioinfo
closed
12 months ago
0
Merge pull request #9 from DavisLaboratory/master
#10
ningbioinfo
closed
1 year ago
0
merge from master
#9
ningbioinfo
closed
1 year ago
0
Unclear how sampleAnnoFile & featureAnnoFile are derived (arguments to readGeoMx function)
#8
cjstepek
closed
10 months ago
2
vignette update
#7
ningbioinfo
closed
1 year ago
1
function to transform spe to NanoStringGeoMXSet
#6
ningbioinfo
opened
1 year ago
0
Bug fix
#5
lardenoije
closed
1 year ago
1
connection to NanoStringGeoMxSet object
#4
inijman
closed
1 year ago
1
Add informative error messages.
#3
ningbioinfo
closed
1 year ago
0
Add StatStratum import from ggalluvial and move ggalluvial to imports
#2
kieranrcampbell
closed
1 year ago
1
QC plotting functions
#1
bhuvad
closed
2 years ago
0