2
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2
replies
11k
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scran ScoreMarkers throws a warning
scoreMarkers scran
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by ★ 1.5k
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2
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tximport error in reading salmon output files?
tximport tximportData
updated 22 months ago by • 0 • written 2.5 years ago by • 0
0
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2
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1.3k
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Question regarding FAQ
clusterProfiler
2.5 years ago kl-fr • 0
1
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3
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5.0k
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Making MDS plot
plotMDS limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
4
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4
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1.7k
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DESeq2 lfcShrink function used in DiffBind package
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2.5 years ago bhandary.8590 ▴ 20
0
votes
0
replies
534
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Gene names not included on KEGGgraph plots
KEGGgraph
2.5 years ago hilarius_bookbinder • 0
0
votes
5
replies
1.4k
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 2.5 years ago by • 0
1
vote
0
replies
734
views
News: Bioconductor Website Redesign - We Need Your Input!
Bioconductor Website
2.5 years ago shepherl 4.2k
0
votes
6
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1.5k
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Creating the right number/distribution of sequences in bootranges
bootranges nullranges
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
votes
4
replies
1.5k
views
DESEq2 Error: rows did not converge
DESeq2
2.5 years ago andrebolerbarros ▴ 20
0
votes
3
replies
1.3k
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
votes
2
replies
1.1k
views
Can DESeq2 handle low number of samples and replicates?
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
1
vote
4
replies
2.2k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
2.5 years ago Jiyoung Lee • 0
0
votes
1
reply
1.1k
views
Gene enrichment analysis
analysis R GOfuncR
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by • 0
2
votes
5
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2.4k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 20 months ago by • 0 • written 2.5 years ago by • 0
1
vote
1
reply
1.1k
views
mia package installation has non-zero exit status
mia miaviz
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
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2
replies
1.4k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.6 years ago by ▴ 70
1
vote
4
replies
1.6k
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
written 2.6 years ago by • 0
1
vote
3
replies
1.2k
views
DESeq: relaxing gene filtering thresholds increases mean-Sd correlation, but recovers many important genes
metaanalysis meanSd genefilter DESeq2
2.5 years ago Ndimensional ▴ 20
2
votes
8
replies
2.0k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
2.5 years ago Ndimensional ▴ 20
0
votes
0
replies
463
views
Can I plot values from LINCS level 4?
cmapR
2.5 years ago Alexandre • 0
0
votes
5
replies
1.4k
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
1
reply
527
views
Is there a way to solve "the model matrix is not full rank", when just one of my sample is showing batch effect?
DESeq2
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
17
replies
5.0k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 2.5 years ago by • 0 • written 8.2 years ago by • 0
0
votes
0
replies
1.3k
views
Job: Bioinformatics Spatial Omics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
SpatialExperiment JobPosting
2.5 years ago Peter Hickey ▴ 760
0
votes
1
reply
738
views
DESeq2 how to extract expression values corresponding to log2FoldChange
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
votes
4
replies
3.0k
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BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
1
reply
827
views
Comparing DGE between datasets with uneven sample sizes using DESeq2
unevensamplesizes ComparingDGEresults DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
1
vote
1
reply
729
views
Deseq contrast question
RNASeqData DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 10
0
votes
4
replies
1.3k
views
Using different filtering steps in different iterations of DEseq2
DESeq2
2.5 years ago marinaw ▴ 20
1
vote
0
replies
686
views
Help with error running DiffBind
DiffBind
2.5 years ago Chris ▴ 20
0
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0
replies
1.3k
views
Issues setting background in STRINGdb
STRINGdb MSstats
2.5 years ago samsiljee • 0
0
votes
1
reply
903
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
2.5 years ago Esraa • 0
1
vote
2
replies
948
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
2.5 years ago jovel_juan ▴ 30
1
vote
2
replies
1.1k
views
Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db
hgu133plus2hsentrezg.db chiptype chipster hgu133plus2.db AffymetrixChip
2.5 years ago alexia.brunel • 0
0
votes
2
replies
1.1k
views
Error with IsoformSwitchAnalyzer: analyzePFAM
IsoformSwitchAnalyzeR
updated 14 months ago by • 0 • written 2.5 years ago by • 0
3
votes
7
replies
7.0k
views
error with champ.load
champ
written 8.1 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Can DESeq2 handle huge variations in sequencing depth among samples?
HugevariationsinsequencingDepth DESeq2
2.5 years ago Gopinath • 0
0
votes
1
reply
1.6k
views
multiple filters in biomaRt
biomaRt
updated 2.5 years ago by ▴ 10 • written 2.6 years ago by • 0
0
votes
0
replies
1.1k
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
2.5 years ago Yijing • 0
0
votes
4
replies
2.1k
views
Discrepancy between DESeq2 files produced in Galaxy and R(RStudio)
DESeq2
updated 23 months ago by • 0 • written 2.5 years ago by • 0
0
votes
0
replies
836
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
2.5 years ago nick_brittain55 • 0
0
votes
1
reply
629
views
Several questions about the workflow using DESeq2 to process RNA data
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 20
1
vote
3
replies
5.0k
views
DeSEQ 2 Error: some values in assay are negative
Countmatrix negativeassay DESeq2
2.5 years ago dania.khalid • 0
1
vote
7
replies
2.4k
views
Diffbind "No genome detected"
DiffBind
updated 2.1 years ago by 68k • written 2.5 years ago by • 0
2
votes
3
replies
2.2k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.5 years ago Lluís Revilla Sancho ▴ 760
0
votes
1
reply
734
views
How to use txtimport and do differential expression
NewWave
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
vote
2
replies
1.4k
views
How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
2.5 years ago Irene • 0
0
votes
0
replies
1.1k
views
MAGECK MLE design matrix
mageck MAGeCKFlute
2.5 years ago Monika • 0
0
votes
0
replies
964
views
mzTab-M in XCMS
xcms mzTab-M iterativehierarchicalprocessing FBMN
2.5 years ago Abrianna • 0
46,699 results • Page 50 of 934
Recent ...
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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
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You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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