Showing : SummarizedExperiment • reset
8
votes
23
replies
1.0k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 4 weeks ago by ★ 3.3k • written 4 weeks ago by ▴ 40
0
votes
18
replies
2.6k
views
DESeq2: Possible issue with colData and sorting
deseq2 summarizedexperiment
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 40
0
votes
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 6.0 years ago by 65k • written 6.0 years ago by • 0
3
votes
11
replies
3.0k
views
DESeqDataSetFromMatrix gives a 'dimnames are not identical error' in R 4.0 that worked fine in R 3.6.1.
DESeq2 SummarizedExperiment
updated 21 months ago by • 0 • written 3.3 years ago by ▴ 20
6
votes
11
replies
2.2k
views
MultiAssayExperiment: how to store data for multiple cancer lesions for each patients
multiassayexperiment summarizedexperiment cancer genomics
5.9 years ago mario.zanfardino ▴ 160
1
vote
11
replies
5.4k
views
how to merge SummarizedExperiment datasets
summarizedexperiment
updated 19 months ago by • 0 • written 4.6 years ago by • 0
1
vote
11
replies
2.4k
views
Had to remove duplicated() in order to install GenomicRanges 1.22 on top of 1.20 on linux
installation genomicranges summarizedexperiment
8.6 years ago • updated 8.5 years ago knb • 0
4
votes
11
replies
2.3k
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
2
votes
10
replies
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
5
votes
9
replies
2.0k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
5.8 years ago rbronste ▴ 60
2
votes
8
replies
1.9k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
4.8 years ago Wuschel ▴ 10
1
vote
8
replies
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
votes
8
replies
3.1k
views
Tutorial: "developing" with HDF5Array
hdf5 DelayedArray summarizedexperiment Tutorial
7.3 years ago Vincent J. Carey, Jr. 6.7k
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 9.2 years ago by ★ 13k • written 9.2 years ago by ▴ 30
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
7
replies
1.4k
views
How to filter out low read counts
summarizedExperiment
updated 4.6 years ago by 25k • written 4.6 years ago by • 0
3
votes
7
replies
1.9k
views
biocLite installs older version of SummarizedExperiment package
summarizedexperiment
7.7 years ago gaiusjaugustus • 0
5
votes
7
replies
1.3k
views
featAssayPlotDefaults does not work for SummarizedExperiment object
iSEE SummarizedExperiment
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 20
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
4
votes
6
replies
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
3
votes
6
replies
848
views
Subsetting Range Summarized Experiment
SummarizedExperiment
7 months ago • updated 6 months ago Bine ▴ 40
1
vote
6
replies
1.3k
views
Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
22 months ago BioInfoBeginnerrr • 0
5
votes
6
replies
3.4k
views
How to add a column to metadata in SummarizedExperiment for DESeq2 type objects?
DESeq2 SummarizedExperiment
3.5 years ago • updated 3.4 years ago mschmidt ▴ 10
1
vote
6
replies
1.5k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.2 years ago cosmin • 0
2
votes
5
replies
973
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
5
replies
1.1k
views
Adding SummarizedExperiment function
summarizedexperiment
7.3 years ago rbronste ▴ 60
2
votes
5
replies
1.5k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
20 months ago Marcus • 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 2.5 years ago by • 0
3
votes
5
replies
940
views
calculate distance to a certain sequence in one gene
SummarizedExperiment Genetics
updated 12 months ago by 65k • written 13 months ago by • 0
2
votes
4
replies
1.7k
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
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
2
votes
4
replies
1.7k
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
7.2 years ago Jurat Shahidin ▴ 80
1
vote
4
replies
2.0k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR summarizedexperiment dgelist
6.1 years ago aljoscha.leusmann • 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
2
votes
4
replies
1.3k
views
How to construct a SummarizedExperiment object?
SummarizedExperiment
12 months ago Yijing • 0
1
vote
3
replies
1.6k
views
Merge column to SummarizedExperiment from other dataframe
summarizedexperiment rangedsummarizedexperiment illimina 450k methylation
5.6 years ago s.w.vanderlaan ▴ 30
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 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 30
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
0
votes
3
replies
2.9k
views
Converstion of Ranged Summarized Experiment to Data Frame
SummarizedExperiment RangedSummarizedExperiment
updated 3.6 years ago by ▴ 830 • written 3.6 years ago by • 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 6.5 years ago by 21k • written 6.5 years ago by ▴ 100
0
votes
3
replies
1.2k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 20 months ago by 65k • written 20 months ago by • 0
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
2
votes
3
replies
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
1
vote
2
replies
1.3k
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
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
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
3
votes
2
replies
1.3k
views
Subset SummarizedExperiment Objects by Metadata
summarizedexperiment
6.3 years ago Lucas Schiffer ▴ 240
0
votes
2
replies
1.2k
views
SummarizedExperiment no function found corresponding to methods exports from XVector for concatenateObjects
SummarizedExperiment
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
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
50 results • Page 1 of 1
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Comment: How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups by Gordon Smyth 50k
The NG dispersion is almost zero for your data, meaning that there is almost no biological variation between the replicates. There are also…
Comment: Can I trust the differential expression analysis when the two groups overlap on by BioinfGuru ▴ 30
No worries, wish I could be more help. Plotly provide a [3-D plot][1] function that's pretty simple (the two you did are still 2-D plots, t…
Comment: Can I trust the differential expression analysis when the two groups overlap on by Michael Love 42k
If you manually compute PCA on VST data, what are the top 5 genes contributing to PC1? https://github.com/thelovelab/DESeq2/blob/devel/R/p…
Comment: Can I trust the differential expression analysis when the two groups overlap on by Eric Katagirya • 0
I created a DESeqDataSet object using DESeqDataSetFromMatrix function. I don't anticipate any mismatching or mixup of sampleIDs.
Answer: Assymetric MA plot with no overall trend by Michael Love 42k
> so many upregulated genes vs. downregulated, which I think is worrying Take a look at the plotCounts for a couple of the up-regulated …
Votes
Answer: Can log2cpm be used for proteomics data normalization?
Ensembl 112 has been released.
A: Diffbind results - non uniform width
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Answer: Error EPICv2 ChAMP
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