Ecosyste.ms: Issues

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GitHub / DavisLaboratory/standR issues and pull requests

#40 - ReadGeoMx Issues

Issue - State: open - Opened by ava-amidei about 1 month ago

#38 - Update pcaOtherPlotting.R

Pull Request - State: closed - Opened by dkcoxie 3 months ago - 2 comments

#37 - `readGeoMx` Input from GeoMx NGS Pipeline

Issue - State: closed - Opened by bharatm26 3 months ago - 1 comment

#36 - Normalization method inquiry

Issue - State: closed - Opened by jheonsuh 5 months ago - 1 comment

#35 - Inquiry about Normalization Process

Issue - State: open - Opened by jheonsuh 5 months ago - 1 comment

#34 - Differential expression analysis with limma-voom pipeline

Issue - State: closed - Opened by orange-3711 5 months ago - 1 comment

#33 - PrepareSpatialDecon error message

Issue - State: open - Opened by emiliasiukola 6 months ago - 1 comment

#32 - Using alternative batch correction methods to RUV

Issue - State: open - Opened by Doc-R-J 6 months ago - 1 comment

#31 - SpatialDecon using readGeoMx

Issue - State: open - Opened by jjoo12 7 months ago - 7 comments

#30 - Input file for your own experiment

Issue - State: closed - Opened by willros 7 months ago - 5 comments

#29 - Unable to plot PCA (scater incompatibility?)

Issue - State: closed - Opened by iddryg 7 months ago - 2 comments

#28 - readGeoMx error in rowNames

Issue - State: closed - Opened by kav-ita 8 months ago - 1 comment

#27 - standR Workflow for Cancer Transcriptome Atlas (CTA)

Issue - State: open - Opened by ErickMUO 9 months ago - 2 comments
Labels: enhancement

#25 - Update README.md, add citation

Pull Request - State: closed - Opened by ningbioinfo 11 months ago

#24 - spatialdecon

Issue - State: closed - Opened by OnkarMulay 12 months ago - 1 comment

#23 - issue with prepareSpatialDecon() function

Issue - State: closed - Opened by sciotlos 12 months ago - 2 comments

#22 - add n_assay argument for findBestK

Issue - State: open - Opened by samleenz almost 1 year ago
Labels: enhancement

#21 - Rationale for TPM and RPKM

Issue - State: closed - Opened by ChelseaCHENX about 1 year ago - 1 comment

#20 - `norm.factors` not being transferred from `SpatialExperiment` to `DGEList`

Issue - State: closed - Opened by jaredmcollette over 1 year ago - 1 comment
Labels: enhancement

#19 - readGeoMx error invalid 'row.names' length

Issue - State: closed - Opened by RLau0 over 1 year ago - 1 comment

#18 - Error in readGeoMx qith rmNegProbe = FALSE

Issue - State: closed - Opened by Sigmatilde over 1 year ago - 1 comment

#17 - plotRLExpr() looking for region annotation

Issue - State: closed - Opened by Sigmatilde over 1 year ago - 1 comment

#16 - Error in readGeoMx

Issue - State: closed - Opened by knadia07 over 1 year ago - 8 comments

#15 - bug fix: plotting bugs and preparedecon bug

Pull Request - State: closed - Opened by ningbioinfo over 1 year ago

#14 - removebatcheffect removal and normalization

Issue - State: closed - Opened by dksenthil over 1 year ago - 1 comment

#13 - plotScreePCA and plotPCAbiplot with reducedDim

Issue - State: closed - Opened by joonlee3 over 1 year ago - 1 comment

#12 - Extract normalized expression matrix

Issue - State: closed - Opened by GeremyClair over 1 year ago - 2 comments

#11 - add propeller-related function, link it to the deconvolution output.

Issue - State: closed - Opened by ningbioinfo over 1 year ago
Labels: enhancement

#10 - Merge pull request #9 from DavisLaboratory/master

Pull Request - State: closed - Opened by ningbioinfo over 1 year ago

#9 - merge from master

Pull Request - State: closed - Opened by ningbioinfo over 1 year ago

#7 - vignette update

Issue - State: closed - Opened by ningbioinfo over 1 year ago - 1 comment
Labels: enhancement

#6 - function to transform spe to NanoStringGeoMXSet

Issue - State: open - Opened by ningbioinfo almost 2 years ago
Labels: enhancement

#5 - Bug fix

Pull Request - State: closed - Opened by lardenoije almost 2 years ago - 1 comment

#4 - connection to NanoStringGeoMxSet object

Issue - State: closed - Opened by inijman over 2 years ago - 1 comment

#3 - Add informative error messages.

Issue - State: closed - Opened by ningbioinfo over 2 years ago
Labels: enhancement

#2 - Add StatStratum import from ggalluvial and move ggalluvial to imports

Pull Request - State: closed - Opened by kieranrcampbell over 2 years ago - 1 comment

#1 - QC plotting functions

Pull Request - State: closed - Opened by bhuvad over 2 years ago