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
5.8 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 18 months ago by • 0 • written 4.6 years ago by • 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
7.2 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
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 4.5 years ago by ▴ 60
5
votes
8
replies
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
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Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS bsseq summarizedexperiment
8.6 years ago Tim Peters ▴ 170
4
votes
2
replies
1.2k
views
MultiAssayExperiment wideformat operations
multiassayexperiment summarizedexperiment wide format
updated 5.8 years ago by ★ 1.1k • written 5.8 years ago by ▴ 160
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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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 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 20
3
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6
replies
759
views
Subsetting Range Summarized Experiment
SummarizedExperiment
6 months ago Bine ▴ 40
1
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8
replies
2.7k
views
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
1
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4
replies
4.3k
views
Running DESeqDataSet with 4 factors?
summarizedexperiment deseq2 deseqdataset multiple factor design differential gene expression
8.7 years ago Lillyhchen ▴ 10
4
votes
11
replies
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
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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
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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
reply
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
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1
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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 6.4 years ago by ★ 1.0k • written 6.5 years ago by • 0
10
votes
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
3
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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
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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 5.9 years ago by 65k • written 5.9 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 5.8 years ago by ★ 1.1k • written 5.8 years ago by ▴ 160
0
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1
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2.6k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by • 0
3
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5
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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
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
0
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2
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702
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Excluding samples as referenced in SummarizedExperiment vignette
SummarizedExperiment vignette
2.1 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
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691
views
Error in SummarizedExperiment(...)
SummarizedExperiment StandR
updated 13 months ago by ▴ 70 • written 13 months ago by • 0
2
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4
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1.6k
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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
0
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1
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663
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
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4
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1.2k
views
How to construct a SummarizedExperiment object?
SummarizedExperiment
11 months ago Yijing • 0
3
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5
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915
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calculate distance to a certain sequence in one gene
SummarizedExperiment Genetics
updated 12 months ago by 65k • written 12 months ago by • 0
0
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1
reply
1.8k
views
DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
2
votes
5
replies
898
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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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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