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Plotting genomic interactions in Gviz
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9.7 years ago enricoferrero ▴ 680
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Error in readCtData
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9.7 years ago lizhensor • 0
0
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2
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Same or different tools: AnnotationHub and AnnotationDbi?
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updated 9.7 years ago by 25k • written 9.7 years ago by • 0
5
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5
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Using p.nominal DE genes from limma
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updated 9.7 years ago by ▴ 370 • written 9.7 years ago by ▴ 420
0
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1
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Fluidigm data analysis - how to get adj p-values for 96 genes
fluidigm wilcoxon signed rank test t.test adj.p.value normal distribution
updated 9.7 years ago by 53k • written 9.8 years ago by • 0
0
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1
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1.3k
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RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 80
1
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34
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6.4k
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how to check which probesets belong to which transcript?
xps affymetrix microarrays humangene2.0ST micro array data
updated 9.7 years ago by ★ 3.9k • written 9.8 years ago by ▴ 120
10
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10
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Method for batch correction
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updated 9.7 years ago by ▴ 120 • written 9.8 years ago by ▴ 60
0
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2
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2.1k
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Duplicated rows in readVcf output
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updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by • 0
5
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1
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4.0k
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Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread rsubread ensembldb Tutorial
9.7 years ago phil.chapman ▴ 150
1
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4
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1.6k
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calculate total transcript length from DisjointExons output (Genomic Ranges Object)
genomicfeatures non overlapping exons genomicranges granges
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 30
2
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4
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DESeq2 normFactors method: Error in fitBetaWrapper
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9.7 years ago Jakub ▴ 50
1
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6
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4.5k
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Map between Manufacturer Identifiers and Gene Symbol
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9.8 years ago • updated 9.7 years ago maedakus ▴ 10
0
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1
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2.5k
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Missing the package called 'R.oo'. Please help me to fix, thanks.
TCGAbiolinks
updated 9.7 years ago by ▴ 150 • written 9.7 years ago by • 0
6
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5
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Is filtering necessary to extract significant DE genes with limma ?
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updated 9.7 years ago by 53k • written 9.7 years ago by ▴ 40
0
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2
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1.8k
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labelling limma volcano plot interactively
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updated 9.7 years ago by 53k • written 9.7 years ago by ▴ 20
0
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0
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1.1k
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lymphGate Preselection Argument
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9.7 years ago alee • 0
2
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9
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3.7k
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bumphunter beta values
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updated 9.7 years ago by 68k • written 9.7 years ago by ▴ 50
2
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1
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1.9k
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Update bioconductor in R 3.2.4
GenomicRanges biocupgrade
updated 9.7 years ago by ★ 8.2k • written 9.7 years ago by ▴ 40
6
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6
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6.4k
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Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
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updated 9.7 years ago by 43k • written 9.8 years ago by • 0
1
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3
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2.3k
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PCA clusters by replicates not by study groups
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9.8 years ago stolarek.ir • 0
1
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3
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1.6k
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AnnotationDBI Select with incomplete keys tags
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9.8 years ago Rockbar • 0
10
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9
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2.7k
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Overriding of shrinkage in DESeq2
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updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 90
0
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7
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2.3k
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VariantAnnotation produces duplicate names
variantannotation
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ▴ 40
1
vote
13
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7.6k
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"Over-correction" in the size-factors of the DESeq2 package
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9.8 years ago gil.hornung • 0
3
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6
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4.2k
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Pool Single-cells: Analysis
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updated 9.8 years ago by ★ 29k • written 9.8 years ago by ▴ 90
9
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6
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13k
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Error bars DESeq or DESeq2 fold change
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updated 4.2 years ago by 43k • written 9.8 years ago by ▴ 10
4
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1
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4.6k
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PCA plot on DE genes do not separate samples. DESeq2.
deseq2 pca
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 10
10
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2
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Possible to incorporate the sign or direction of an effect in the IHW covariate?
IHW
updated 9.8 years ago by ▴ 180 • written 9.8 years ago by ▴ 60
9
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7
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2.4k
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EdgeR returns small logFC values when using GLM approach
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9.8 years ago gergely.zsuzsa.n • 0
0
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0
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1.3k
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Protein structure prediction
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9.8 years ago ashamscsoft • 0
1
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2
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DESeq2 performance information for counts tables with very large rows number
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9.8 years ago atisou • 0
0
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0
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Nimblegen DNA methylation microarray data analysis
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9.8 years ago mail.jyotim • 0
0
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0
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error while running MAplot
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9.8 years ago kritikamish99 ▴ 10
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built vignette using knitr
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9.8 years ago kmezhoud ▴ 10
2
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export BSgenome directly in gzipped fasta
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updated 9.8 years ago by ▴ 90 • written 9.8 years ago by ▴ 80
0
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2
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time course experiment with many time points in limmc for Rna-seq data
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9.8 years ago Joanna Zyprych ▴ 20
0
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1
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1.8k
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LuminalA Breast cancer subtype samples from GEO GSE62944
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updated 9.8 years ago by ▴ 150 • written 9.8 years ago by • 0
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1.3k
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get the vector of leaf's names from object "dendrogram" generated by cut()
updated 9.8 years ago by • 0 • written 20.9 years ago by ▴ 250
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Importing and Extracting Annotation
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updated 9.8 years ago by 68k • written 9.8 years ago by • 0
3
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Batch effects in limma
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updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
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GCRMA segmentation fault
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updated 9.8 years ago by 68k • written 9.8 years ago by • 0
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6
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difficulty loading rsbml
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updated 9.8 years ago by • 0 • written 14.9 years ago by ★ 1.1k
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10
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Package lists and other questions about the site
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9.8 years ago george.carlisle • 0
2
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2
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limma making contrasts appropriately
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updated 9.8 years ago by ★ 13k • written 9.8 years ago by ▴ 20
4
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6
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goseq: not able to limit by GO categories when using wallenius approximation for over-representation test
goseq
updated 9.8 years ago by ▴ 320 • written 9.8 years ago by ▴ 10
1
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2
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2.2k
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ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 9.8 years ago by 25k • written 9.8 years ago by ▴ 150
1
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0
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1.5k
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Job: Industry Postdoc at EMBL: Statistical Computing in Multi-Omics and Drug Target Validation
job Job
9.8 years ago Wolfgang Huber ★ 13k
3
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2
replies
1.9k
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Why does requireNamespace("org.Hs.eg.db") load DBI and RSQLite?
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updated 9.8 years ago by 25k • written 9.8 years ago by 53k
0
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5
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3.1k
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How to get list of genes that are DE from the goseq analysis results
limma goseq mget edgeR
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 10
46,711 results • Page 401 of 935
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Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
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A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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