Showing : summarizedExperiment • reset
1
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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
6
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11
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2.2k
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MultiAssayExperiment: how to store data for multiple cancer lesions for each patients
multiassayexperiment summarizedexperiment cancer genomics
5.9 years ago mario.zanfardino ▴ 160
1
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11
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5.3k
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how to merge SummarizedExperiment datasets
summarizedexperiment
updated 19 months ago by • 0 • written 4.6 years ago by • 0
0
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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
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
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
2
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5
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1.1k
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Adding SummarizedExperiment function
summarizedexperiment
7.3 years ago rbronste ▴ 60
3
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8
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3.0k
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Tutorial: "developing" with HDF5Array
hdf5 DelayedArray summarizedexperiment Tutorial
7.2 years ago Vincent J. Carey, Jr. 6.7k
1
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6
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1.3k
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Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
22 months ago • updated 21 months ago BioInfoBeginnerrr • 0
1
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3
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1.6k
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Merge column to SummarizedExperiment from other dataframe
summarizedexperiment rangedsummarizedexperiment illimina 450k methylation
5.5 years ago s.w.vanderlaan ▴ 30
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 ★ 5.2k • written 4.6 years ago by ▴ 60
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
2
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10
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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
1
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8
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1.9k
views
SummarizedExperiment Error! expressionSet data structure
software error summarizedexperiment
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 20
3
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2
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1.3k
views
Subset SummarizedExperiment Objects by Metadata
summarizedexperiment
6.3 years ago Lucas Schiffer ▴ 240
0
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2
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2.1k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
8.7 years ago • updated 8.6 years ago Tim Peters ▴ 170
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
5
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9
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1.9k
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DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
5.8 years ago rbronste ▴ 60
1
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2
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1.2k
views
Extending SummarizedExperiment without rowRanges argument
summarizedexperiment rangedsummarizedexperiment
updated 5.5 years ago by 25k • written 5.5 years ago by • 0
4
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6
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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
2
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2
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1.0k
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
3
votes
6
replies
794
views
Subsetting Range Summarized Experiment
SummarizedExperiment
6 months ago Bine ▴ 40
1
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8
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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
1
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4
replies
4.3k
views
Running DESeqDataSet with 4 factors?
summarizedexperiment deseq2 deseqdataset multiple factor design differential gene expression
8.8 years ago Lillyhchen ▴ 10
4
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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
3
votes
3
replies
1.8k
views
How to initialize a SummarizedExperiment?
summarizedexperiment SummarizedExperiment
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 90
2
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2
replies
1.2k
views
Cannot load old SummarizedExperiment in R 3.3, Bioc 3.3
summarizedexperiment backwards compatibility
updated 7.9 years ago by 16k • written 7.9 years ago by ★ 7.9k
3
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3
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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
3
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7
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1.9k
views
biocLite installs older version of SummarizedExperiment package
summarizedexperiment
7.6 years ago gaiusjaugustus • 0
2
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1
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4.0k
views
DESeq2 error when creating the DESeqDataSet
deseq2 bioconductor deseqdataset r summarizedexperiment
7.5 years ago sebastian.lobentanzer ▴ 50
1
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2
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1.2k
views
rowRanges in Summarized Experiment changes counts
deseq2 summarizedexperiment rangedsummarizedexperiment rnaseq
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 10
3
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3
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1.5k
views
How to construct an up-to-date and annotation-rich RangeSummarizedExperiment object around old microarray data?
geoquery summarizedexperiment rangedsummarizedexperiment
updated 6.5 years ago by 21k • written 6.5 years ago by ▴ 100
0
votes
1
reply
1.2k
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Getting pheno tables from recount datasets without any NA values in characteristics and geo_accession fields and also without duplicated row.names
recount summarizedexperiment
updated 6.5 years ago by ★ 1.0k • written 6.5 years ago by • 0
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
3
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2
replies
1.3k
views
Difficulty creating SummarizedExperiment
summarizedexperiment
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 10
0
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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 65k • written 6.0 years ago by • 0
1
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1
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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
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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 ★ 4.1k • written 2.7 years ago by • 0
3
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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
4
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4
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1.4k
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
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2
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716
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Excluding samples as referenced in SummarizedExperiment vignette
SummarizedExperiment vignette
2.2 years ago BioInfoBeginnerrr • 0
0
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3
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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
0
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1
reply
710
views
Error in SummarizedExperiment(...)
SummarizedExperiment StandR
updated 14 months ago by ▴ 70 • written 14 months ago by • 0
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 11 months ago by 16k • written 11 months ago by ▴ 90
0
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1
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681
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
2
votes
4
replies
1.2k
views
How to construct a SummarizedExperiment object?
SummarizedExperiment
12 months ago • updated 11 months ago Yijing • 0
3
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5
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928
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
1
reply
1.9k
views
DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
2
votes
5
replies
923
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
2
votes
3
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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
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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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