Showing : summarizedExperiment • reset
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
7 weeks ago • updated 25 days ago info ▴ 10
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343
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Rstudio died when put more than three letters in subseting a SummarizedExperiment object
SummarizedExperiment
9 weeks ago Shuo GG • 0
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23
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2.9k
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Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 7 months ago by ★ 3.4k • written 7 months ago by ▴ 50
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5
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1.6k
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SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 12 months ago by 43k • written 12 months ago by • 0
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6
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Subsetting Range Summarized Experiment
SummarizedExperiment
13 months ago Bine ▴ 50
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4
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2.3k
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SummarizedExperiment is now warning on attach about `read_block` namespace conflict
SummarizedExperiment S4Arrays DelayedArray
updated 17 months ago by 16k • written 18 months ago by ▴ 90
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4
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How to construct a SummarizedExperiment object?
SummarizedExperiment
18 months ago Yijing • 0
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5
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1.2k
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calculate distance to a certain sequence in one gene
SummarizedExperiment Genetics
updated 19 months ago by 67k • written 19 months ago by • 0
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2
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789
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Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 20 months ago by • 0 • written 20 months ago by • 0
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1.1k
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Error in SummarizedExperiment(...)
SummarizedExperiment StandR
updated 21 months ago by ▴ 70 • written 21 months ago by • 0
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1
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2.5k
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DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 22 months ago by ★ 4.5k • written 22 months ago by • 0
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11
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6.3k
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how to merge SummarizedExperiment datasets
summarizedexperiment
updated 2.1 years ago by • 0 • written 5.2 years ago by • 0
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1
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937
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How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 2.2 years ago by 67k • written 2.2 years ago by • 0
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3
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1.6k
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Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 2.2 years ago by 67k • written 2.2 years ago by • 0
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5
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Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
2.2 years ago Marcus • 0
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2
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1.1k
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conditional command within GRanges
SummarizedExperiment
updated 2.3 years ago by 700 • written 2.3 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
2.4 years ago BioInfoBeginnerrr • 0
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0
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673
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Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
2.5 years ago syednajeebashraf • 0
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Excluding samples as referenced in SummarizedExperiment vignette
SummarizedExperiment vignette
2.7 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 3.0 years ago by 43k • written 3.1 years ago by • 0
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779
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Fastest way to work with a large RangedSummarizedExperiment object
SummarizedExperiment summ
3.2 years ago alexgutteridge ▴ 50
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1
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3.2k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.3 years ago by ★ 4.5k • written 3.3 years ago by • 0
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4
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1.8k
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How to save multiple assays and subsequent processed data in single SummarizedExperiment Object
SummarizedExperiment
updated 3.6 years ago by 1.6k • written 3.6 years ago by ▴ 20
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1
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2.2k
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
3.7 years ago Matthias Munz ▴ 20
3
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11
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3.5k
views
DESeqDataSetFromMatrix gives a 'dimnames are not identical error' in R 4.0 that worked fine in R 3.6.1.
DESeq2 SummarizedExperiment
updated 2.3 years ago by • 0 • written 3.9 years ago by ▴ 20
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6
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How to add a column to metadata in SummarizedExperiment for DESeq2 type objects?
DESeq2 SummarizedExperiment
4.0 years ago mschmidt ▴ 10
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3
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3.5k
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Converstion of Ranged Summarized Experiment to Data Frame
SummarizedExperiment RangedSummarizedExperiment
updated 4.1 years ago by ▴ 830 • written 4.1 years ago by • 0
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7
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1.5k
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featAssayPlotDefaults does not work for SummarizedExperiment object
iSEE SummarizedExperiment
updated 4.6 years ago by ★ 28k • written 4.6 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 5.0 years ago by 25k • written 5.0 years ago by ▴ 10
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3
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1.7k
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Filtering counts in SummarizedExperiment
diffbind matrix summarizedexperiment rangedCounts
updated 5.1 years ago by ★ 5.2k • written 5.1 years ago by ▴ 60
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7
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1.7k
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How to filter out low read counts
summarizedExperiment
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
2
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8
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2.4k
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Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
5.3 years ago Wuschel ▴ 10
2
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3
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1.7k
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"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 5.4 years ago by ★ 13k • written 5.4 years ago by ▴ 30
1
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8
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3.0k
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DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
2
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10
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4.1k
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Help: how to use wilcox.test with a SummarizedExperiment object?
Wilcoxon-Mann-Whitney test SummarizedExperiment Wilcoxon-Mann-Whitney test
updated 2.8 years ago by • 0 • written 5.5 years ago by • 0
6
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1.5k
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News: Winners of the 1st Shiny Contest: iSEE
iSEE shiny summarizedExperiment News
5.6 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
5.6 years ago gerald.mccollam • 0
2
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2
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1.3k
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SetMethod to dispatch on class in unattached package
s4 methods SummarizedExperiment
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 20
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6
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1.9k
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How to best represent weights in SummarizedExperiment or SingleCellExperiment?
SummarizedExperiment SingleCellExperiment
updated 5.9 years ago by ▴ 980 • written 5.9 years ago by ▴ 100
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2
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1.4k
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Extending SummarizedExperiment without rowRanges argument
summarizedexperiment rangedsummarizedexperiment
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
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3
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1.9k
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Merge column to SummarizedExperiment from other dataframe
summarizedexperiment rangedsummarizedexperiment illimina 450k methylation
6.1 years ago s.w.vanderlaan ▴ 30
5
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9
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2.2k
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DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
6.3 years ago rbronste ▴ 60
6
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11
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2.6k
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MultiAssayExperiment: how to store data for multiple cancer lesions for each patients
multiassayexperiment summarizedexperiment cancer genomics
6.4 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 6.4 years ago by ★ 1.1k • written 6.4 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 6.4 years ago by ★ 1.1k • written 6.4 years ago by ▴ 160
0
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13
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2.2k
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R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list concatenation of SummarizedExperiment
summarizedexperiment bug 3.5.0
updated 6.5 years ago by 67k • written 6.5 years ago by • 0
1
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4
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2.4k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR summarizedexperiment dgelist
6.6 years ago aljoscha.leusmann • 0
1
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6
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1.8k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.7 years ago cosmin • 0
3
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2
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1.5k
views
Difficulty creating SummarizedExperiment
summarizedexperiment
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 10
3
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2
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1.5k
views
Subset SummarizedExperiment Objects by Metadata
summarizedexperiment
6.8 years ago Lucas Schiffer ▴ 240
50 results • Page 1 of 1
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Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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