Showing : summarizedexperiment • reset
8
votes
23
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1.1k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 6 weeks ago by ★ 3.3k • written 6 weeks ago by ▴ 40
2
votes
5
replies
1.1k
views
SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 6 months ago by 42k • written 6 months ago by • 0
3
votes
6
replies
880
views
Subsetting Range Summarized Experiment
SummarizedExperiment
7 months ago Bine ▴ 40
2
votes
4
replies
1.8k
views
SummarizedExperiment is now warning on attach about `read_block` namespace conflict
SummarizedExperiment S4Arrays DelayedArray
updated 11 months ago by 16k • written 12 months ago by ▴ 90
2
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4
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1.3k
views
How to construct a SummarizedExperiment object?
SummarizedExperiment
12 months ago Yijing • 0
3
votes
5
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955
views
calculate distance to a certain sequence in one gene
SummarizedExperiment Genetics
updated 13 months ago by 66k • written 13 months ago by • 0
0
votes
2
replies
596
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 14 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
734
views
Error in SummarizedExperiment(...)
SummarizedExperiment StandR
updated 15 months ago by ▴ 70 • written 15 months ago by • 0
0
votes
1
reply
1.9k
views
DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
1
vote
11
replies
5.5k
views
how to merge SummarizedExperiment datasets
summarizedexperiment
updated 20 months ago by • 0 • written 4.7 years ago by • 0
0
votes
1
reply
722
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 20 months ago by 66k • written 20 months ago by • 0
0
votes
3
replies
1.2k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 20 months ago by 66k • written 20 months ago by • 0
2
votes
5
replies
1.5k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
21 months ago Marcus • 0
1
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2
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895
views
conditional command within GRanges
SummarizedExperiment
updated 21 months ago by 700 • written 21 months ago by • 0
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 22 months ago by • 0 • written 3.4 years ago by ▴ 20
1
vote
6
replies
1.3k
views
Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
22 months ago BioInfoBeginnerrr • 0
0
votes
0
replies
558
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
24 months ago syednajeebashraf • 0
0
votes
2
replies
733
views
Excluding samples as referenced in SummarizedExperiment vignette
SummarizedExperiment vignette
2.2 years ago BioInfoBeginnerrr • 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 2.3 years ago by • 0 • written 5.0 years ago by • 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 42k • written 2.6 years ago by • 0
0
votes
0
replies
650
views
Fastest way to work with a large RangedSummarizedExperiment object
SummarizedExperiment summ
2.7 years ago alexgutteridge ▴ 50
0
votes
1
reply
2.7k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.8 years ago by ★ 4.2k • written 2.8 years ago by • 0
4
votes
4
replies
1.5k
views
How to save multiple assays and subsequent processed data in single SummarizedExperiment Object
SummarizedExperiment
updated 3.1 years ago by 1.6k • written 3.1 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
3.2 years ago Matthias Munz ▴ 10
5
votes
6
replies
3.4k
views
How to add a column to metadata in SummarizedExperiment for DESeq2 type objects?
DESeq2 SummarizedExperiment
3.5 years ago mschmidt ▴ 10
0
votes
3
replies
2.9k
views
Converstion of Ranged Summarized Experiment to Data Frame
SummarizedExperiment RangedSummarizedExperiment
updated 3.6 years ago by ▴ 830 • written 3.6 years ago by • 0
5
votes
7
replies
1.3k
views
featAssayPlotDefaults does not work for SummarizedExperiment object
iSEE SummarizedExperiment
updated 4.1 years ago by ★ 28k • written 4.1 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 4.5 years ago by 25k • written 4.5 years ago by ▴ 10
2
votes
3
replies
1.4k
views
Filtering counts in SummarizedExperiment
diffbind matrix summarizedexperiment rangedCounts
updated 4.6 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 4.6 years ago by 25k • written 4.6 years ago by • 0
2
votes
8
replies
2.0k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.8 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 4.9 years ago by ★ 13k • written 4.9 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
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
1.1k
views
SetMethod to dispatch on class in unattached package
s4 methods SummarizedExperiment
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
4
votes
6
replies
1.6k
views
How to best represent weights in SummarizedExperiment or SingleCellExperiment?
SummarizedExperiment SingleCellExperiment
updated 5.4 years ago by ▴ 950 • written 5.4 years ago by ▴ 100
1
vote
2
replies
1.2k
views
Extending SummarizedExperiment without rowRanges argument
summarizedexperiment rangedsummarizedexperiment
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
1
vote
3
replies
1.7k
views
Merge column to SummarizedExperiment from other dataframe
summarizedexperiment rangedsummarizedexperiment illimina 450k methylation
5.6 years ago s.w.vanderlaan ▴ 30
5
votes
9
replies
2.0k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
5.8 years ago rbronste ▴ 60
6
votes
11
replies
2.3k
views
MultiAssayExperiment: how to store data for multiple cancer lesions for each patients
multiassayexperiment summarizedexperiment cancer genomics
5.9 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
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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 66k • written 6.0 years ago by • 0
1
vote
4
replies
2.1k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR summarizedexperiment dgelist
6.1 years ago aljoscha.leusmann • 0
1
vote
6
replies
1.5k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.2 years ago cosmin • 0
3
votes
2
replies
1.3k
views
Difficulty creating SummarizedExperiment
summarizedexperiment
updated 6.2 years ago by ★ 28k • written 6.2 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
2.5k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 6.4 years ago by 21k • written 6.4 years ago by ▴ 60
0
votes
0
replies
1.3k
views
DEXseq: error using DEXSeqDataSetFromSE command
rnaseq dexseq summarizedexperiment
6.5 years ago f.carlisle • 0
50 results • Page 1 of 1
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Replies
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
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