Showing : summarizedexperiment • reset
1
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how to merge SummarizedExperiment datasets
summarizedexperiment
updated 18 months ago by • 0 • written 4.6 years ago by • 0
1
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4
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4.3k
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Running DESeqDataSet with 4 factors?
summarizedexperiment deseq2 deseqdataset multiple factor design differential gene expression
8.7 years ago Lillyhchen ▴ 10
2
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1
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4.0k
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DESeq2 error when creating the DESeqDataSet
deseq2 bioconductor deseqdataset r summarizedexperiment
7.4 years ago sebastian.lobentanzer ▴ 50
2
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10
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3.4k
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
5
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8
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3.3k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment DESeqDataSet GenomicRanges DESeq2 save
updated 9.2 years ago by ★ 13k • written 9.2 years ago by ▴ 30
5
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6
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3.2k
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How to add a column to metadata in SummarizedExperiment for DESeq2 type objects?
DESeq2 SummarizedExperiment
3.4 years ago • updated 3.3 years ago mschmidt ▴ 10
3
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8
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3.0k
views
Tutorial: "developing" with HDF5Array
hdf5 DelayedArray summarizedexperiment Tutorial
7.2 years ago Vincent J. Carey, Jr. 6.7k
3
votes
11
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2.9k
views
DESeqDataSetFromMatrix gives a 'dimnames are not identical error' in R 4.0 that worked fine in R 3.6.1.
DESeq2 SummarizedExperiment
updated 20 months ago by • 0 • written 3.3 years ago by ▴ 20
0
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3
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2.7k
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Converstion of Ranged Summarized Experiment to Data Frame
SummarizedExperiment RangedSummarizedExperiment
updated 3.5 years ago by ▴ 830 • written 3.5 years ago by • 0
1
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8
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2.7k
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DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 4.8 years ago by 25k • written 4.8 years ago by • 0
0
votes
18
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2.6k
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DESeq2: Possible issue with colData and sorting
deseq2 summarizedexperiment
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 40
0
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1
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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
10
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7
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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
1
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11
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2.4k
views
Had to remove duplicated() in order to install GenomicRanges 1.22 on top of 1.20 on linux
installation genomicranges summarizedexperiment
8.5 years ago • updated 8.4 years ago knb • 0
4
votes
11
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2.3k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by ▴ 10
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
0
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2
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2.1k
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Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
8.6 years ago Tim Peters ▴ 170
1
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4
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2.0k
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edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR summarizedexperiment dgelist
6.0 years ago aljoscha.leusmann • 0
5
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9
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1.9k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
5.7 years ago rbronste ▴ 60
1
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8
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1.9k
views
SummarizedExperiment Error! expressionSet data structure
software error summarizedexperiment
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 20
2
votes
8
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1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.7 years ago Wuschel ▴ 10
3
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7
replies
1.9k
views
biocLite installs older version of SummarizedExperiment package
summarizedexperiment
7.6 years ago gaiusjaugustus • 0
0
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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 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
1
reply
1.8k
views
DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
3
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3
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1.8k
views
How to initialize a SummarizedExperiment?
summarizedexperiment SummarizedExperiment
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 90
0
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1
reply
1.7k
views
Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
3.1 years ago Matthias Munz ▴ 10
2
votes
4
replies
1.7k
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
7.1 years ago Jurat Shahidin ▴ 80
2
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4
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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
1
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3
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1.6k
views
Merge column to SummarizedExperiment from other dataframe
summarizedexperiment rangedsummarizedexperiment illimina 450k methylation
5.5 years ago s.w.vanderlaan ▴ 30
4
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6
replies
1.6k
views
How to best represent weights in SummarizedExperiment or SingleCellExperiment?
SummarizedExperiment SingleCellExperiment
updated 5.2 years ago by ▴ 950 • written 5.2 years ago by ▴ 100
0
votes
1
reply
1.5k
views
Error invalid class "SummarizedExperiment" when using library("MultiDataSet")
summarizedexperiment rangedsummarizedexperiment multidataset
6.6 years ago s.w.vanderlaan ▴ 30
1
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6
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1.5k
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deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.1 years ago cosmin • 0
3
votes
3
replies
1.5k
views
How to construct an up-to-date and annotation-rich RangeSummarizedExperiment object around old microarray data?
geoquery summarizedexperiment rangedsummarizedexperiment
updated 6.4 years ago by 21k • written 6.4 years ago by ▴ 100
0
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2
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1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
2
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3
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1.5k
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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 4.7 years ago by ★ 13k • written 4.7 years ago by ▴ 30
3
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5
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1.4k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 2.4 years ago by 41k • written 2.4 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
1
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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
5
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1.4k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
19 months ago Marcus • 0
2
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3
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1.4k
views
Filtering counts in SummarizedExperiment
diffbind matrix summarizedexperiment rangedCounts
updated 4.5 years ago by ★ 5.1k • written 4.5 years ago by ▴ 60
3
votes
2
replies
1.3k
views
Subset SummarizedExperiment Objects by Metadata
summarizedexperiment
6.2 years ago Lucas Schiffer ▴ 240
0
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0
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1.3k
views
DEXseq: error using DEXSeqDataSetFromSE command
rnaseq dexseq summarizedexperiment
6.4 years ago f.carlisle • 0
6
votes
0
replies
1.3k
views
News: Winners of the 1st Shiny Contest: iSEE
iSEE shiny summarizedExperiment News
5.0 years ago Aaron Lun ★ 28k
3
votes
2
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1.3k
views
Difficulty creating SummarizedExperiment
summarizedexperiment
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 10
0
votes
0
replies
1.2k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
5.0 years ago gerald.mccollam • 0
1
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6
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1.2k
views
Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
21 months ago BioInfoBeginnerrr • 0
5
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7
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1.2k
views
featAssayPlotDefaults does not work for SummarizedExperiment object
iSEE SummarizedExperiment
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 20
1
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2
replies
1.2k
views
rowRanges in Summarized Experiment changes counts
deseq2 summarizedexperiment rangedsummarizedexperiment rnaseq
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 10
0
votes
2
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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
3
votes
3
replies
1.2k
views
aggregate bins in large SummarizedExperiment efficiently
granges summarizedexperiment reduce
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you Michael for your attention to my question. I am truly grateful. I subsetted the data using lines of codes to include only the g…
Comment: [DiffBind] Obtaining normalization factors by Henry ▴ 10
I see, thank you for your suggestion! I managed to use a separate RLE normalization to obtain the size factors.
Answer: Memory errors using read.bismark? by Peter Hickey ▴ 690
Thanks for sharing an example file. This is a very large non-CpG methylation dataset, which are tricky to work with for a number of reason…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by Peter Hickey ▴ 690
Superficially, your issue is similar to [https://github.com/hansenlab/bsseq/issues/136](https://github.com/hansenlab/bsseq/issues/136). You…
Votes
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
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