Showing : summarizedExperiment • reset
8
votes
23
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874
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 16 days ago by ★ 3.3k • written 17 days ago by ▴ 40
2
votes
5
replies
908
views
SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 5 months ago by 41k • written 5 months ago by • 0
3
votes
6
replies
778
views
Subsetting Range Summarized Experiment
SummarizedExperiment
6 months ago Bine ▴ 40
2
votes
4
replies
1.6k
views
SummarizedExperiment is now warning on attach about `read_block` namespace conflict
SummarizedExperiment S4Arrays DelayedArray
updated 10 months ago by 16k • written 11 months ago by ▴ 90
2
votes
4
replies
1.2k
views
How to construct a SummarizedExperiment object?
SummarizedExperiment
11 months ago Yijing • 0
3
votes
5
replies
922
views
calculate distance to a certain sequence in one gene
SummarizedExperiment Genetics
updated 12 months ago by 65k • written 12 months ago by • 0
0
votes
2
replies
575
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 13 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
700
views
Error in SummarizedExperiment(...)
SummarizedExperiment StandR
updated 14 months ago by ▴ 70 • written 14 months ago by • 0
0
votes
1
reply
1.8k
views
DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
1
vote
11
replies
5.3k
views
how to merge SummarizedExperiment datasets
summarizedexperiment
updated 19 months ago by • 0 • written 4.6 years ago by • 0
0
votes
1
reply
672
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 19 months ago by 65k • written 19 months ago by • 0
0
votes
3
replies
1.1k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 19 months ago by 65k • written 19 months ago by • 0
2
votes
5
replies
1.4k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
20 months ago Marcus • 0
1
vote
2
replies
875
views
conditional command within GRanges
SummarizedExperiment
updated 20 months ago by 690 • written 20 months ago by • 0
1
vote
6
replies
1.3k
views
Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
21 months ago BioInfoBeginnerrr • 0
0
votes
0
replies
538
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
23 months ago syednajeebashraf • 0
0
votes
2
replies
707
views
Excluding samples as referenced in SummarizedExperiment vignette
SummarizedExperiment vignette
2.1 years ago BioInfoBeginnerrr • 0
3
votes
5
replies
1.5k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
0
votes
0
replies
628
views
Fastest way to work with a large RangedSummarizedExperiment object
SummarizedExperiment summ
2.6 years ago alexgutteridge ▴ 50
0
votes
1
reply
2.6k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by • 0
4
votes
4
replies
1.4k
views
How to save multiple assays and subsequent processed data in single SummarizedExperiment Object
SummarizedExperiment
updated 3.0 years ago by 1.6k • written 3.0 years ago by ▴ 20
0
votes
1
reply
1.8k
views
Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
3.1 years ago Matthias Munz ▴ 10
3
votes
11
replies
3.0k
views
DESeqDataSetFromMatrix gives a 'dimnames are not identical error' in R 4.0 that worked fine in R 3.6.1.
DESeq2 SummarizedExperiment
updated 21 months ago by • 0 • written 3.3 years ago by ▴ 20
5
votes
6
replies
3.3k
views
How to add a column to metadata in SummarizedExperiment for DESeq2 type objects?
DESeq2 SummarizedExperiment
3.4 years ago mschmidt ▴ 10
0
votes
3
replies
2.8k
views
Converstion of Ranged Summarized Experiment to Data Frame
SummarizedExperiment RangedSummarizedExperiment
updated 3.5 years ago by ▴ 830 • written 3.5 years ago by • 0
5
votes
7
replies
1.3k
views
featAssayPlotDefaults does not work for SummarizedExperiment object
iSEE SummarizedExperiment
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 20
0
votes
2
replies
1.2k
views
SummarizedExperiment no function found corresponding to methods exports from XVector for concatenateObjects
SummarizedExperiment
updated 4.4 years ago by 25k • written 4.4 years ago by ▴ 10
2
votes
3
replies
1.4k
views
Filtering counts in SummarizedExperiment
diffbind matrix summarizedexperiment rangedCounts
updated 4.5 years ago by ★ 5.2k • written 4.6 years ago by ▴ 60
1
vote
7
replies
1.4k
views
How to filter out low read counts
summarizedExperiment
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.7 years ago Wuschel ▴ 10
2
votes
3
replies
1.5k
views
"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
GenomicRanges rtracklayer VariantAnnotation S4Vectors SummarizedExperiment
updated 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 30
1
vote
8
replies
2.7k
views
DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
2
votes
10
replies
3.5k
views
Help: how to use wilcox.test with a SummarizedExperiment object?
Wilcoxon-Mann-Whitney test SummarizedExperiment Wilcoxon-Mann-Whitney test
updated 2.2 years ago by • 0 • written 4.9 years ago by • 0
6
votes
0
replies
1.3k
views
News: Winners of the 1st Shiny Contest: iSEE
iSEE shiny summarizedExperiment News
5.1 years ago Aaron Lun ★ 28k
0
votes
0
replies
1.3k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
5.1 years ago gerald.mccollam • 0
2
votes
2
replies
1.0k
views
SetMethod to dispatch on class in unattached package
s4 methods SummarizedExperiment
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 20
4
votes
6
replies
1.6k
views
How to best represent weights in SummarizedExperiment or SingleCellExperiment?
SummarizedExperiment SingleCellExperiment
updated 5.3 years ago by ▴ 950 • written 5.3 years ago by ▴ 100
1
vote
2
replies
1.2k
views
Extending SummarizedExperiment without rowRanges argument
summarizedexperiment rangedsummarizedexperiment
updated 5.5 years ago by 25k • written 5.5 years ago by • 0
1
vote
3
replies
1.6k
views
Merge column to SummarizedExperiment from other dataframe
summarizedexperiment rangedsummarizedexperiment illimina 450k methylation
5.5 years ago s.w.vanderlaan ▴ 30
5
votes
9
replies
1.9k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
5.7 years ago rbronste ▴ 60
6
votes
11
replies
2.2k
views
MultiAssayExperiment: how to store data for multiple cancer lesions for each patients
multiassayexperiment summarizedexperiment cancer genomics
5.8 years ago mario.zanfardino ▴ 160
4
votes
2
replies
1.2k
views
MultiAssayExperiment wideformat operations
multiassayexperiment summarizedexperiment wide format
updated 5.9 years ago by ★ 1.1k • written 5.9 years ago by ▴ 160
1
vote
1
reply
1.0k
views
subsets different type of data together
R multiassayexperiment rangedsummarizedexperiment summarizedexperiment
updated 5.9 years ago by ★ 1.1k • written 5.9 years ago by ▴ 160
0
votes
13
replies
1.9k
views
R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list concatenation of SummarizedExperiment
summarizedexperiment bug 3.5.0
updated 6.0 years ago by 65k • written 6.0 years ago by • 0
1
vote
4
replies
2.0k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR summarizedexperiment dgelist
6.0 years ago aljoscha.leusmann • 0
1
vote
6
replies
1.5k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.1 years ago cosmin • 0
3
votes
2
replies
1.3k
views
Difficulty creating SummarizedExperiment
summarizedexperiment
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 10
3
votes
2
replies
1.3k
views
Subset SummarizedExperiment Objects by Metadata
summarizedexperiment
6.3 years ago Lucas Schiffer ▴ 240
10
votes
7
replies
2.4k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 6.3 years ago by 21k • written 6.3 years ago by ▴ 60
0
votes
0
replies
1.3k
views
DEXseq: error using DEXSeqDataSetFromSE command
rnaseq dexseq summarizedexperiment
6.4 years ago f.carlisle • 0
50 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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