2
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2
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1.9k
views
How does Deseq2 deal with the row with zero when calculating size factors
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written 2.0 years ago by • 0
1
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2
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1.2k
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RNASeq time course analysis, missing time points for control
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2.0 years ago drewhaydensteele • 0
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8
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GOslim missing GO term
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2.0 years ago amanda • 0
0
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3
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Obtaining rsIDs with ENSG and variant ID information
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updated 2.0 years ago by ★ 3.4k • written 2.0 years ago by ▴ 30
8
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7
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2.4k
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Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
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1
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2
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1.4k
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EdgeR: Exact test and glmQLFTest produce very different results
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updated 2.0 years ago by 53k • written 2.0 years ago by • 0
12
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5
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limma::voom vs edgeR::voomLmFit - when to use?
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updated 6 months ago by • 0 • written 2.0 years ago by • 0
2
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1.2k
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NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
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2.0 years ago R_Page • 0
1
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1
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965
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updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
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How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
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updated 2.0 years ago by ★ 4.1k • written 2.0 years ago by • 0
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1
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654
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analysis of overexpressed proteins in metaproteomes
Proteomics ProteoMM ProteomicsWorkflow Proteome
written 2.0 years ago by ▴ 10
0
votes
0
replies
574
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Rgraphviz - exported (toFile) dot file loses colour and label information
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2.0 years ago sterlinggunn01 • 0
1
vote
2
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
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2.1 years ago • updated 24 months ago Levi • 0
0
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0
replies
717
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multipollutant models
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2.1 years ago Jitendra ▴ 10
4
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4
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5.0k
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How should I run ssGSEA Hallmark Enrichment Analysis?
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1
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0
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666
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Attempting to import SBML file using R
SBMLR sbml rsbm rsbml
updated 2.0 years ago by 43k • written 2.1 years ago by ▴ 10
0
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1
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824
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SingleR Book Not Found
SingleR
updated 2.1 years ago by ▴ 760 • written 2.1 years ago by • 0
3
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2
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1.3k
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tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
3
replies
948
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bam or VCF files from GSE75010
splots CopyNumberVariationData
written 2.1 years ago by • 0
0
votes
3
replies
1.3k
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'Subtracting' counts on basis of Negative control media and water samples
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2.1 years ago • updated 2.0 years ago Karthik • 0
0
votes
5
replies
1.2k
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 70
3
votes
6
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Result from GSEA for non-model organism not as expected
clusterProfiler
updated 2.1 years ago by 68k • written 3.2 years ago by ▴ 10
0
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3
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2.7k
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
2.1 years ago Oenone • 0
0
votes
2
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convert sequences disambiguated with DECIPHER back to FASTA
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written 5.5 years ago by • 0
3
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8
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DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
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written 2.1 years ago by ▴ 10
4
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6
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Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 21 months ago by • 0 • written 2.1 years ago by ▴ 10
0
votes
0
replies
998
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help with converting MSTRG tags with isoformswictanalyzer
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updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
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1
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624
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Lower FDR cutoff gives more gene counts
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
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1
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782
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Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
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updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
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1
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750
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Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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849
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How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
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861
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DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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2
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Help Subsetting DDS for plotPCA for contrast groups
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2.1 years ago • updated 2.0 years ago yee • 0
4
votes
12
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2.5k
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Ensembl down???
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2.1 years ago • updated 2.0 years ago bas_work ▴ 30
0
votes
2
replies
983
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2.1 years ago Tom ▴ 10
0
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1
reply
758
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In the 'About_Annotation_Packages_org.Sc.sgd.db_3.17' columns("org.Sc.sgd.db"), the 'CHRLOC' information is not displayed. However, the 'index.txt' f…
org.Sc.sgd.db
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
5
replies
4.0k
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Cannot connect to ExperimentHub server
ExperimentHub
updated 19 months ago by • 0 • written 2.1 years ago by • 0
0
votes
9
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It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
2.1 years ago nromerov • 0
0
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3
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1.2k
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Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
2.1 years ago claire • 0
0
votes
2
replies
827
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WGCNA less samples
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2.1 years ago davca • 0
0
votes
0
replies
727
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Cannot read biom file in R
RESOLVE
updated 2.1 years ago by 4.2k • written 2.1 years ago by • 0
1
vote
1
reply
634
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Minimum datasets needed for meta analysis
RnaSeqSampleSize
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by ▴ 10
2
votes
3
replies
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
2.1 years ago Karthik • 0
2
votes
1
reply
747
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DataFrame Printing User Control
S4Vectors
updated 2.1 years ago by 16k • written 2.1 years ago by ★ 1.6k
3
votes
2
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biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl biomaRt
2.1 years ago henrydionne ▴ 10
3
votes
4
replies
1.4k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.1 years ago pl23 • 0
0
votes
0
replies
638
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Normalising processed Proteomics data in R
Bioconductor Proteomics
2.1 years ago Joshua • 0
0
votes
1
reply
921
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Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
2
votes
5
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STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 20 months ago by ▴ 110 • written 2.1 years ago by • 0
0
votes
2
replies
977
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FlowSOM error system.file()
FlowSOM
updated 2.1 years ago by ▴ 360 • written 2.1 years ago by • 0
46,696 results • Page 37 of 934
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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