3
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3
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2.8k
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EnsDb.Rnorvegicus for Rnor6
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updated 5.5 years ago by ★ 4.1k • written 5.5 years ago by • 0
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1
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1.3k
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mircomb analysis from deg's list
mircomb mrna mirna degs interaction
5.5 years ago andreia ▴ 10
0
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2
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mirna-mrna interation mircomb (from DEGs and DEMs lists)
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updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
12
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5
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5.5k
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Rsamtools is not available for (for R version 4.0.2)
Rsamtools
updated 17 months ago by • 0 • written 5.5 years ago by ▴ 40
4
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6
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Extremely big genes in annotation TxDb packages
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updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
0
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3
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886
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DESeq2 Design Model and Results Function Set-Up - How to know if using the interaction term is appropriate?
deseq2 rnaseq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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1
reply
1.1k
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How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
1
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3
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758
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MAplots after lfcshrink
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updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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1
reply
1.8k
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do expression of leading edges within a negative NES term reflect the same direction as it's enrichment score? aka downregulation of leading edges
fgsea
updated 5.5 years ago by ▴ 280 • written 5.5 years ago by ▴ 30
0
votes
0
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782
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According to SCBN method, is it possible to acquire normalized data for virtualziation?
SCBN normalization
5.5 years ago tofukaj • 0
5
votes
11
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Visualization tool for GC-bias in SE data?
GC-bias ALPINE visualization
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 20
2
votes
6
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2.0k
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Why is an averaged reference used in DESeq2 normalisation?
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updated 5.5 years ago by ★ 29k • written 5.5 years ago by • 0
1
vote
1
reply
906
views
A question for clarification regarding counts input to DESeqDataSetFromMatrix
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 60
1
vote
2
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1.3k
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EdgeR blocking factor - missing paired sample
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updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 60
0
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4
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3.0k
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Error: unexpected string constant in "suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE)), when installed the package "Mus.musculus"…
install packages Mus.musculus
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
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0
replies
771
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What values to include for predictedMethNull in BiSeq
Biseq
5.5 years ago akhaira • 0
0
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0
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1.2k
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Job: Senior Postdoc/Bioinformatician Research Fellow @ UEA, Norwich, UK - New deadline
cancer nextgenerationsequencing prostate Job
5.9 years ago • updated 5.5 years ago Daniel Brewer ▴ 100
4
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6
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Using spike-in RNA for normalization of Salmon counts imported using Tximport
deseq2 Tximport Sizefactors normalizationfactors spike-in
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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0
replies
856
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ViseaGO merge_enrich_terms ERROR
go
5.5 years ago zaza.inline • 0
0
votes
2
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14k
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ComplexHeatmap - how to change the position of the legend of rowAnnotation
ComplexHeatmap
updated 7 months ago by ▴ 10 • written 5.5 years ago by • 0
1
vote
1
reply
911
views
Obtain Protein-Protein Interaction (PPI) table from a list of Gene IDs in R or Python.
Protein Protein Interaction Gene List BioGRID PICKLE R Programming
5.5 years ago omarrafiqued ▴ 50
1
vote
2
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1.9k
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"Error in nbinomLRT(... less than one degree of freedom"... Isolating main and interaction effects with the LRT?
deseq2 main effects interaction effects R lrt
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
9
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4.8k
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WGCNA module trait relationship issue
wgcna
updated 5.5 years ago by ★ 3.0k • written 5.5 years ago by • 0
7
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4
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2.4k
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How does BiocParallel export variables to threads?
BiocParallel SnowParam parallel
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 170
1
vote
3
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1.8k
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Package DECHIPER successfully downloaded but not installed
DECHIPER unsuccessfull installation
updated 5.5 years ago by ▴ 160 • written 5.5 years ago by • 0
4
votes
5
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1.8k
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Custom Functional for automated DESeq2 running
deseq2
updated 5.5 years ago by ★ 1.4k • written 5.5 years ago by ▴ 20
0
votes
2
replies
1.9k
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Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
2
replies
2.3k
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DESeq2 doubts about transformations + nbinomWaldtest warning
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updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
5
votes
9
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7.3k
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Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray affy
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 40
0
votes
2
replies
27k
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Installing EnhancedVolcano package in R
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updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
votes
0
replies
987
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Pathview colors only matching ids?
pathview
5.5 years ago okna0215 ▴ 10
1
vote
1
reply
1.3k
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
2
replies
2.1k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
4
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6.0k
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ggplot2 of PCA
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updated 5.5 years ago by • 0 • written 5.6 years ago by ▴ 20
1
vote
2
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3.1k
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News: Bioc2020 - Call for BOF/HAK/FAQ Sections
conference bioc2020 talks deadline News
5.8 years ago • updated 5.5 years ago shepherl 4.2k
1
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0
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1.4k
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Pathview : why are some genes not colored?
pathview rna-seq
5.5 years ago okna0215 ▴ 10
0
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6
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2.7k
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Workaround to using normalized counts as input for edgeR
edger
updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 40
0
votes
7
replies
25k
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DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
1
reply
1.5k
views
ropls package: Recreating scores calculation from an OPLS-DA model
ropls
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
votes
0
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News: Bioc2020 - Call for BOF/HAK/FAQ Sections Still Open
conference bioc2020 talks News
5.5 years ago shepherl 4.2k
2
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6
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3.5k
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How to run tximport ?
tximport
updated 5.5 years ago by ★ 5.0k • written 5.5 years ago by • 0
0
votes
0
replies
751
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How can I fix and run "sigCVError" function ?
sigFeature svm-rfe sigCVError feature selection
5.5 years ago rekren ▴ 20
3
votes
9
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7.5k
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DESeq2: Clarification on independent filtering threshold values
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 20
1
vote
12
replies
2.1k
views
Taking much longer time for same script after R upgrade to 4.0
R
5.5 years ago hsiowa2 ▴ 20
1
vote
2
replies
1.4k
views
question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq single-cell tutorial
updated 5.5 years ago by ★ 29k • written 5.5 years ago by • 0
1
vote
1
reply
629
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Unable to run tximport using sample.info ?
tximport deseq2 edgeR
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
4
replies
1.9k
views
tximport importer isoform abundance
tximport
updated 2.6 years ago by ▴ 200 • written 5.5 years ago by ▴ 620
2
votes
2
replies
2.7k
views
Using GSVA All the pathway score are same
GSVA scRNA-seq data
updated 5.5 years ago by ★ 3.4k • written 5.5 years ago by • 0
3
votes
5
replies
1.2k
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How to loop over two files ...and calculate R^2 between SNPs
loops R
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
3
votes
2
replies
1.1k
views
Differential methylation analysis and paired samples
edger bisulfite sequencing
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
46,710 results • Page 161 of 935
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Comment: Is it possible to install previous versions of the packages instead of the newes by Lamb • 0
I totally feel you on the struggle to manage package versions! Just last month, I had to roll back a package in R for a project because the…
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Hey there! I stumbled upon your post about the no package called Biobase error, and it really struck a chord with me. I have faced similar …
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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…
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Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
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limma moderated t-statistics and B-statistics
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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
how to control age and gender effect in expression data using DESeq2
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