Showing : summarizedexperiment • reset
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
3 months ago • updated 10 weeks ago info ▴ 10
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377
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Rstudio died when put more than three letters in subseting a SummarizedExperiment object
SummarizedExperiment
3 months ago Shuo GG • 0
8
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23
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3.3k
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Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 9 months ago by ★ 3.4k • written 9 months ago by ▴ 50
2
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5
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1.8k
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SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 14 months ago by 43k • written 14 months ago by • 0
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6
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Subsetting Range Summarized Experiment
SummarizedExperiment
15 months ago Bine ▴ 50
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4
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2.4k
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SummarizedExperiment is now warning on attach about `read_block` namespace conflict
SummarizedExperiment S4Arrays DelayedArray
updated 19 months ago by 16k • written 20 months ago by ▴ 90
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4
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How to construct a SummarizedExperiment object?
SummarizedExperiment
20 months ago Yijing • 0
3
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5
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calculate distance to a certain sequence in one gene
SummarizedExperiment Genetics
updated 21 months ago by 67k • written 21 months ago by • 0
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2
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812
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Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 21 months ago by • 0 • written 22 months ago by • 0
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1.2k
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Error in SummarizedExperiment(...)
SummarizedExperiment StandR
updated 22 months ago by ▴ 70 • written 22 months ago by • 0
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1
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2.7k
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DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 23 months ago by ★ 4.6k • written 24 months ago by • 0
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11
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6.5k
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how to merge SummarizedExperiment datasets
summarizedexperiment
updated 2.3 years ago by • 0 • written 5.3 years ago by • 0
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1
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962
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How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 2.3 years ago by 67k • written 2.3 years ago by • 0
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3
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1.7k
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Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 2.3 years ago by 67k • written 2.3 years ago by • 0
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5
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Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
2.4 years ago Marcus • 0
1
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2
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1.2k
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conditional command within GRanges
SummarizedExperiment
updated 2.4 years ago by 700 • written 2.4 years ago by • 0
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6
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1.6k
views
Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
2.5 years ago BioInfoBeginnerrr • 0
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0
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692
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Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
2.6 years ago syednajeebashraf • 0
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Excluding samples as referenced in SummarizedExperiment vignette
SummarizedExperiment vignette
2.9 years ago BioInfoBeginnerrr • 0
3
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5
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1.9k
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Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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801
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Fastest way to work with a large RangedSummarizedExperiment object
SummarizedExperiment summ
3.3 years ago alexgutteridge ▴ 50
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1
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3.3k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.4 years ago by ★ 4.6k • written 3.4 years ago by • 0
4
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4
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1.9k
views
How to save multiple assays and subsequent processed data in single SummarizedExperiment Object
SummarizedExperiment
updated 3.8 years ago by 1.6k • written 3.8 years ago by ▴ 20
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1
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2.3k
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
3.8 years ago Matthias Munz ▴ 20
3
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11
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3.6k
views
DESeqDataSetFromMatrix gives a 'dimnames are not identical error' in R 4.0 that worked fine in R 3.6.1.
DESeq2 SummarizedExperiment
updated 2.5 years ago by • 0 • written 4.0 years ago by ▴ 20
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6
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4.2k
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How to add a column to metadata in SummarizedExperiment for DESeq2 type objects?
DESeq2 SummarizedExperiment
4.1 years ago mschmidt ▴ 10
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3
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3.6k
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Converstion of Ranged Summarized Experiment to Data Frame
SummarizedExperiment RangedSummarizedExperiment
updated 4.3 years ago by ▴ 840 • written 4.3 years ago by • 0
5
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7
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1.6k
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featAssayPlotDefaults does not work for SummarizedExperiment object
iSEE SummarizedExperiment
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 20
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2
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1.4k
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SummarizedExperiment no function found corresponding to methods exports from XVector for concatenateObjects
SummarizedExperiment
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 10
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3
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1.8k
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Filtering counts in SummarizedExperiment
diffbind matrix summarizedexperiment rangedCounts
updated 5.2 years ago by ★ 5.2k • written 5.3 years ago by ▴ 60
1
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7
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1.8k
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How to filter out low read counts
summarizedExperiment
updated 5.2 years ago by 25k • written 5.2 years ago by • 0
2
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8
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2.5k
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Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.5 years ago Wuschel ▴ 10
2
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3
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1.8k
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 5.5 years ago by ★ 13k • written 5.5 years ago by ▴ 30
1
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8
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3.1k
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DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
2
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10
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4.2k
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Help: how to use wilcox.test with a SummarizedExperiment object?
Wilcoxon-Mann-Whitney test SummarizedExperiment Wilcoxon-Mann-Whitney test
updated 2.9 years ago by • 0 • written 5.6 years ago by • 0
6
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0
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1.5k
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News: Winners of the 1st Shiny Contest: iSEE
iSEE shiny summarizedExperiment News
5.8 years ago Aaron Lun ★ 28k
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1.4k
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TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
5.8 years ago gerald.mccollam • 0
2
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2
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1.4k
views
SetMethod to dispatch on class in unattached package
s4 methods SummarizedExperiment
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 20
4
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6
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2.0k
views
How to best represent weights in SummarizedExperiment or SingleCellExperiment?
SummarizedExperiment SingleCellExperiment
updated 6.0 years ago by ▴ 980 • written 6.0 years ago by ▴ 100
1
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2
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1.5k
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Extending SummarizedExperiment without rowRanges argument
summarizedexperiment rangedsummarizedexperiment
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
1
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3
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2.0k
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Merge column to SummarizedExperiment from other dataframe
summarizedexperiment rangedsummarizedexperiment illimina 450k methylation
6.2 years ago s.w.vanderlaan ▴ 30
5
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9
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2.3k
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DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
6.5 years ago rbronste ▴ 60
6
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11
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2.7k
views
MultiAssayExperiment: how to store data for multiple cancer lesions for each patients
multiassayexperiment summarizedexperiment cancer genomics
6.6 years ago mario.zanfardino ▴ 160
4
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2
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1.4k
views
MultiAssayExperiment wideformat operations
multiassayexperiment summarizedexperiment wide format
updated 6.6 years ago by ★ 1.1k • written 6.6 years ago by ▴ 160
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1
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1.2k
views
subsets different type of data together
R multiassayexperiment rangedsummarizedexperiment summarizedexperiment
updated 6.6 years ago by ★ 1.1k • written 6.6 years ago by ▴ 160
0
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13
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2.2k
views
R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list concatenation of SummarizedExperiment
summarizedexperiment bug 3.5.0
updated 6.7 years ago by 67k • written 6.7 years ago by • 0
1
vote
4
replies
2.5k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR summarizedexperiment dgelist
6.7 years ago aljoscha.leusmann • 0
1
vote
6
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1.8k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.8 years ago cosmin • 0
3
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2
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1.5k
views
Difficulty creating SummarizedExperiment
summarizedexperiment
updated 6.9 years ago by ★ 28k • written 6.9 years ago by ▴ 10
3
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2
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1.5k
views
Subset SummarizedExperiment Objects by Metadata
summarizedexperiment
7.0 years ago Lucas Schiffer ▴ 240
50 results • Page 1 of 1
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Comment: Differential variability modelling with vst() expression by convincing.shark.jqvy • 0
Your approach to differential variability modeling using vst() looks promising! It mirrors the challenge of mastering levels in [Geometry D…
Answer: DESeq2 Heatmap by James W. MacDonald 67k
Two things. First, `scale` is already vectorized, so you don't have to use `apply`. You can instead just do `t(scale(t(mat)))` . Second, th…
Answer: Improve performance of qusage aggregateGeneSet by James W. MacDonald 67k
This support site is meant mostly to help people with questions about using Bioconductor packages rather than posting code improvements. I …
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Votes
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
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