0
votes
1
reply
1.4k
views
Diagnosing topGo issue - single enriched gene per enriched GO term
topGo gene enrichment ontology analysis
6.5 years ago s.bourne • 0
0
votes
3
replies
1.5k
views
lmFit very slow if there are missing values
limma
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 30
0
votes
4
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3.2k
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EdgeR mistake- dispersion
edger
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
0
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1
reply
1.2k
views
use differences in expression as input for co-expression network?
wgcna co-expression
updated 6.5 years ago by ▴ 280 • written 6.6 years ago by ▴ 50
0
votes
4
replies
1.5k
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 90
0
votes
1
reply
1.1k
views
Determining survival correlation among probes
annotation probe microarray
6.5 years ago sbrackett007 • 0
3
votes
2
replies
1.6k
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flowWorkspace cannot load external data
flowWorkspace external data flowCore
6.5 years ago Brent.OCarrigan • 0
0
votes
3
replies
1.9k
views
windows tximport fail
tximport rhdf5
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
1
reply
884
views
How to make a GPos subclass that accept both UnstitchedGPos and StitchedGPos inputs?
GenomicRanges
updated 6.5 years ago by 16k • written 6.6 years ago by ▴ 180
1
vote
2
replies
1.4k
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
6.5 years ago liruiradiant • 0
2
votes
1
reply
1.0k
views
Unintended grey dot in Gviz plots
Gviz
updated 6.5 years ago by ▴ 750 • written 6.5 years ago by ▴ 10
6
votes
4
replies
4.1k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 670
0
votes
1
reply
1.3k
views
"unused argument" error metaMS
metaMS
updated 6.5 years ago by ▴ 20 • written 6.5 years ago by • 0
0
votes
3
replies
2.4k
views
GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
6.5 years ago sandeep.amberkar18 ▴ 10
2
votes
4
replies
1.1k
views
Identifying cell line-independent DEG in a time series (DESeq2)
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
2
replies
2.0k
views
ATACseqQC function bamSplit returns error when input .bam is from mouse
ATACseqQC
6.5 years ago beiting ▴ 30
0
votes
0
replies
673
views
readVcf: duplicated records produced importing 1kG vcf
software error
6.5 years ago sskimb ▴ 10
2
votes
1
reply
1.6k
views
Limma Design matrix for time series+treatment+batch effect
limma factorial design matrix microarray
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
1
vote
5
replies
2.6k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
2
replies
1.5k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 6.5 years ago by ★ 3.6k • written 6.5 years ago by • 0
0
votes
4
replies
2.9k
views
DESeq2 pairwise comparison vs contrast function
deseq2
6.5 years ago dequattro.concetta ▴ 10
1
vote
2
replies
1.3k
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
8
replies
2.3k
views
trackViewer, the interactive version, can't view negative values in bigWig
trackViewer
updated 6.5 years ago by ★ 1.3k • written 6.5 years ago by • 0
0
votes
3
replies
1.1k
views
could the result of DEseq2 by LRT be used in SPIA directly?
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Any recommended workflow for incrementally selecting top ranked genes by using mRMR feature selection?
microarray gene-filtering mRMR parallel-processing bioconductor-package
6.5 years ago Jurat Shahidin ▴ 80
1
vote
2
replies
2.7k
views
Dealing With Package Sizes Greater than 5 MB
data package submission BiocCheck
6.5 years ago j.flesch ▴ 10
0
votes
1
reply
955
views
Choosing Gene ontology package
go annotation GOenrichment
updated 6.5 years ago by ▴ 760 • written 6.5 years ago by • 0
3
votes
3
replies
1.7k
views
Clarification of results tables in DEP
DEP proteomics
updated 6.5 years ago by ▴ 70 • written 6.6 years ago by ▴ 510
2
votes
8
replies
3.2k
views
Error: se does not inherit from class SummarizedExperiment
DEP SummarizedExperiment
6.5 years ago Wuschel ▴ 10
5
votes
13
replies
9.7k
views
DESeq2 for multiple groups
deseq2
updated 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 10
0
votes
3
replies
1.8k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 6.5 years ago by ▴ 70 • written 6.5 years ago by • 0
0
votes
1
reply
1.6k
views
package 'hgu95av2.db' is not available (for R version 3.6.0)
Go.db hgu95av2.db R3.6.0
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
0
replies
684
views
Removing zero counts before normalisation
SCnorm"
6.5 years ago edona • 0
0
votes
5
replies
5.5k
views
Cannot install GO.db for R 3.6.1
GO.db R 3.6.1 source package
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
3
votes
5
replies
1.3k
views
Multifactor design in DESeq2 - infection effect over time on three different plant cultivars
quinoa virus mutifactor design DESeq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
4
replies
2.1k
views
Extract residuals from DESeq2 fit
deseq2 residuals
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
6
replies
2.4k
views
xcms centwave roiList error
roiList xcms centwave XIC
updated 6.5 years ago by ★ 2.1k • written 6.5 years ago by ▴ 10
4
votes
4
replies
1.9k
views
Extracting Data from MSn experiment data ("OnDiskMSnExp")
MSnbase
updated 6.5 years ago by 1.6k • written 6.5 years ago by ▴ 20
3
votes
2
replies
1.5k
views
Access list of rtime/intensity values from chromatograms object from MSnbase
MSnbase chromatograms intensity
updated 6.5 years ago by 1.6k • written 6.5 years ago by ▴ 10
0
votes
0
replies
795
views
correlation coefficient and p value_bicor function_cor.test
cor or bicor function from WGCNA
6.5 years ago tg369 ▴ 40
3
votes
2
replies
9.2k
views
ComplexHeatmap removes row labels if annotation is added
annotation show_row_names complexheatmap
6.5 years ago alexw858 • 0
4
votes
5
replies
1.8k
views
diffBind: differentially bound sites are highly different between using EDGER and DESEQ2
diffbind
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
0
votes
1
reply
2.6k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
6.5 years ago anahochmanova • 0
0
votes
2
replies
5.6k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by • 0
2
votes
2
replies
3.1k
views
How to append cluster and UMAP data to a flowSet?
flow cytometry flowSet UMAP .fcs files
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by • 0
12
votes
7
replies
5.6k
views
Plot ggplot2 and ggbio Images Together
ggplot2 ggbio cowplot
updated 6.5 years ago by ★ 1.5k • written 10.7 years ago by ▴ 370
0
votes
0
replies
1.2k
views
using gene expression matrix for TCseq package to cluster genes
TCseq microwarray cluster counts normalization
6.5 years ago bioyas ▴ 10
0
votes
1
reply
700
views
SELEX-seq NRLB package
software error
6.5 years ago aliceathan • 0
1
vote
3
replies
1.2k
views
Problem to update packages
update problem
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 10
1
vote
2
replies
3.0k
views
flowCore issue: creating and applying new compensation matrix
compensate() flowCore
6.5 years ago rdlr • 0
46,742 results • Page 202 of 935
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Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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