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
8.6 years ago • updated 8.5 years ago knb • 0
6
votes
11
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2.3k
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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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5.5k
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how to merge SummarizedExperiment datasets
summarizedexperiment
updated 20 months ago by • 0 • written 4.7 years ago by • 0
0
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18
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2.7k
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DESeq2: Possible issue with colData and sorting
deseq2 summarizedexperiment
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 40
1
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6
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1.6k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.2 years ago cosmin • 0
1
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4
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2.1k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR summarizedexperiment dgelist
6.1 years ago aljoscha.leusmann • 0
2
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5
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1.1k
views
Adding SummarizedExperiment function
summarizedexperiment
7.3 years ago rbronste ▴ 60
3
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8
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3.1k
views
Tutorial: "developing" with HDF5Array
hdf5 DelayedArray summarizedexperiment Tutorial
7.3 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 BioInfoBeginnerrr • 0
1
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3
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1.7k
views
Merge column to SummarizedExperiment from other dataframe
summarizedexperiment rangedsummarizedexperiment illimina 450k methylation
5.6 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 4.6 years ago by ★ 5.2k • written 4.6 years ago by ▴ 60
5
votes
8
replies
3.4k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment DESeqDataSet GenomicRanges DESeq2 save
updated 9.3 years ago by ★ 13k • written 9.3 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 2.3 years ago by • 0 • written 5.0 years ago by • 0
1
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8
replies
2.0k
views
SummarizedExperiment Error! expressionSet data structure
software error summarizedexperiment
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 20
3
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2
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1.4k
views
Subset SummarizedExperiment Objects by Metadata
summarizedexperiment
6.3 years ago Lucas Schiffer ▴ 240
0
votes
2
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2.2k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
8.7 years ago Tim Peters ▴ 180
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
replies
2.0k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
5.8 years ago rbronste ▴ 60
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
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
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
3
votes
6
replies
888
views
Subsetting Range Summarized Experiment
SummarizedExperiment
7 months ago Bine ▴ 40
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
1
vote
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
votes
11
replies
2.4k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 8.3 years ago by ★ 6.8k • written 8.3 years ago by ▴ 10
3
votes
3
replies
1.8k
views
How to initialize a SummarizedExperiment?
summarizedexperiment SummarizedExperiment
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 90
2
votes
2
replies
1.2k
views
Cannot load old SummarizedExperiment in R 3.3, Bioc 3.3
summarizedexperiment backwards compatibility
updated 8.0 years ago by 16k • written 8.0 years ago by ★ 7.9k
3
votes
3
replies
1.2k
views
aggregate bins in large SummarizedExperiment efficiently
granges summarizedexperiment reduce
updated 7.7 years ago by ★ 11k • written 7.7 years ago by ▴ 20
3
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7
replies
1.9k
views
biocLite installs older version of SummarizedExperiment package
summarizedexperiment
7.7 years ago gaiusjaugustus • 0
2
votes
1
reply
4.1k
views
DESeq2 error when creating the DESeqDataSet
deseq2 bioconductor deseqdataset r summarizedexperiment
7.6 years ago sebastian.lobentanzer ▴ 50
1
vote
2
replies
1.3k
views
rowRanges in Summarized Experiment changes counts
deseq2 summarizedexperiment rangedsummarizedexperiment rnaseq
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 10
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 6.6 years ago by 21k • written 6.6 years ago by ▴ 100
0
votes
1
reply
1.2k
views
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 ★ 1.1k • written 6.6 years ago by • 0
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
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
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 66k • written 6.0 years ago by • 0
1
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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
1
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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
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
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
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2
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736
views
Excluding samples as referenced in SummarizedExperiment vignette
SummarizedExperiment vignette
2.2 years ago BioInfoBeginnerrr • 0
0
votes
3
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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
0
votes
1
reply
739
views
Error in SummarizedExperiment(...)
SummarizedExperiment StandR
updated 15 months ago by ▴ 70 • written 15 months ago by • 0
2
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4
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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
0
votes
1
reply
725
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
2
votes
4
replies
1.3k
views
How to construct a SummarizedExperiment object?
SummarizedExperiment
12 months ago Yijing • 0
3
votes
5
replies
957
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
1
reply
2.0k
views
DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
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
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
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Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
Answer: Error in render R qmd document (could not find function "process") by James W. MacDonald 66k
If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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