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Rsubread align every slow in mac but faster in windows
Rsubread
2.6 years ago
Wei
• 0
3
votes
4
replies
5.7k
views
ComplexHeatmap - Default distance and hierarchical clustering methods
ComplexHeatmap
Complex
updated 2.6 years ago by
elefth.pavlos
▴ 40 • written 2.6 years ago by
Katharina
• 0
0
votes
1
reply
892
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
m-bihie
▴ 10
0
votes
1
reply
3.4k
views
DESeq2 in R 4.2.2
DESeq2
SummarizedExperiment
DelayedArray
updated 2.6 years ago by
ATpoint
★ 4.9k • written 2.6 years ago by
Danielle
• 0
0
votes
3
replies
2.7k
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb
biodbUniprot
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Peter
• 0
0
votes
0
replies
592
views
msa module crash
msa
2.6 years ago
systems
• 0
0
votes
0
replies
873
views
News:
Seeking members for BioC2023 organizing committee
BioC2023
Bioconductor
community
2.6 years ago
Maria Doyle
▴ 100
0
votes
1
reply
1.4k
views
about deltaPSI
SpliceWiz
updated 2.6 years ago by
a.wong
▴ 10 • written 2.6 years ago by
reza.rahman
• 0
2
votes
2
replies
1.3k
views
Volcano Plot in R
cellxgenedp
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Rashi
▴ 10
0
votes
1
reply
1.6k
views
limma: decideTests
affy
limma
affy
limma
updated 2.6 years ago by
Gordon Smyth
53k • written 17.7 years ago by
Al Ivens
▴ 270
0
votes
3
replies
1.3k
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
2.6 years ago
martin.grigorov
▴ 10
0
votes
1
reply
2.8k
views
convert local downloaded bigwig files to .bed files
BRgen
BRGenomics
updated 2.6 years ago by
ATpoint
★ 4.9k • written 2.6 years ago by
kavator
▴ 30
0
votes
1
reply
650
views
NAs in some genes in topTable output
limma
topTable
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
thkapell
▴ 10
0
votes
1
reply
1.1k
views
limma on spectral data
limma
Metabolomics
DifferentialExpression
POMA
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
wiscoyogi
• 0
0
votes
1
reply
988
views
Libraries loading error
DESeq2
clusterProfiler
enrichplot
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
joanna
• 0
0
votes
2
replies
2.8k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 16 months ago by
maria.soler
• 0 • written 2.6 years ago by
kalavattam
▴ 10
4
votes
8
replies
4.2k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
updated 13 months ago by
callumjcparr
• 0 • written 2.6 years ago by
Bernardo
▴ 10
0
votes
1
reply
1.1k
views
Subset count data in DGEList using edgeR/DESeq2
edgeR
DMR
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Fiona
• 0
0
votes
2
replies
1.4k
views
scanBam
Rsamtools
Rsam
updated 2.6 years ago by
Martin Morgan
25k • written 2.6 years ago by
jojo.valensi
• 0
2
votes
3
replies
2.5k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db
AnnotationDbi
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
harish
• 0
0
votes
0
replies
534
views
INSPEcT: How to get the RNA dynamics for steady-state with INSPEcT minus
INSPEcT
2.6 years ago
MK
• 0
0
votes
2
replies
834
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 2.6 years ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
slrpatty
• 0
2
votes
3
replies
2.4k
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.6 years ago by
Stefano Mangiola
▴ 40 • written 6.6 years ago by
ramonmassoni
▴ 10
2
votes
5
replies
1.6k
views
SpliceWiz collateData error
SpliceWiz
updated 15 months ago by
giulia.nicoletto.1
• 0 • written 2.6 years ago by
chiara.caprioli
• 0
2
votes
2
replies
1.1k
views
[DESeq2] There is no difference in expression in my heatmap
DESeq2
heatmaps
2.6 years ago
Sooni
▴ 10
0
votes
0
replies
961
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
2.6 years ago
S
• 0
0
votes
1
reply
998
views
GRanges list convert into igraph format
GRanges
igraph
updated 2.6 years ago by
Lluís Revilla Sancho
▴ 760 • written 2.6 years ago by
Bogdan
▴ 670
0
votes
1
reply
860
views
Extracting interaction contrast when using user supplied model.matrix
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
idetoma
• 0
0
votes
3
replies
1.6k
views
Genes for a given chromosome
GRangesobjectmodification
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Gamal
• 0
0
votes
0
replies
1.0k
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
2.6 years ago
Delta._.43
▴ 20
0
votes
0
replies
931
views
News:
Seeking Outreachy interns and project proposals
Bioconductor
Outreachy
community
2.6 years ago
Maria Doyle
▴ 100
1
vote
3
replies
1.4k
views
DESeq2 Installation Issue
DESeq2
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
joanna
• 0
1
vote
1
reply
696
views
MSc student
genomes
updated 2.6 years ago by
Basti
▴ 780 • written 2.6 years ago by
Deeplaxmi
• 0
0
votes
1
reply
1.2k
views
RUV with K more than 1.
RUVSeq
updated 2.6 years ago by
ATpoint
★ 4.9k • written 2.6 years ago by
star
▴ 10
2
votes
4
replies
1.3k
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2
DifferentialExpression
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
idetoma
• 0
0
votes
1
reply
792
views
Rnaseq analysis using a continuous time series
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Aviads
• 0
0
votes
2
replies
1.7k
views
installing DESeq2 on Macbook R Studio
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Chatura
• 0
0
votes
1
reply
430
views
More information on results columns
DESeq2
updated 2.6 years ago by
ATpoint
★ 4.9k • written 2.6 years ago by
krigerkoalaen
• 0
1
vote
2
replies
4.6k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Keith
• 0
3
votes
4
replies
2.1k
views
Processing data with voom "expression values" and "weights"
limma
voom
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Edmond
• 0
1
vote
1
reply
1.1k
views
how to call an app from Cytoscape using R?
RCy3
updated 2.6 years ago by
alex.pico
▴ 30 • written 2.6 years ago by
adR
▴ 40
0
votes
1
reply
840
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2
RNASeqData
DifferentialExpression
updated 2.6 years ago by
ATpoint
★ 4.9k • written 2.6 years ago by
Julie
• 0
4
votes
4
replies
2.4k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Dario Strbenac
★ 1.6k
1
vote
3
replies
3.6k
views
Do the count values should be only integer to be able to use DESeq2?
DESeq2
2.6 years ago
Sep
• 0
0
votes
1
reply
881
views
Updated package is not the version specified on the homepage
Versions
Update
BindingSiteFinder
updated 2.6 years ago by
Mike Smith
★ 6.6k • written 2.6 years ago by
M.Klostermann
• 0
0
votes
5
replies
1.5k
views
Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2
longitudinal
updated 2.6 years ago by
swbarnes2
★ 1.4k • written 2.6 years ago by
sharvari gujja
▴ 40
1
vote
3
replies
1.9k
views
Adding ellipse in PCAtools biplot
Biplot
FactoMineR
proteomics
PCAtools
ellipse
updated 2.6 years ago by
Kevin Blighe
★ 4.0k • written 2.6 years ago by
M Tuhin
• 0
3
votes
2
replies
986
views
Help with the design matrix for longitudinal study
edgeR
2.6 years ago
sharvari gujja
▴ 40
1
vote
9
replies
2.2k
views
Is it possible to annotate a GRanges Object that has scaffolding names and not chromosome numbers?
Annotation
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
stacy.genovese
• 0
2
votes
4
replies
1.2k
views
Successor of genesBy Defunct Function
ensembldb
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
Dario Strbenac
★ 1.6k
46,615 results • Page
63 of 933
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Replies
Comment: 3-factor DESeq2 trime-series analysis
by
swbarnes2
★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
by
yongjie.wang
• 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
by
Michael Love
43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi
by
Michael Love
43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values
by
Gordon Smyth
53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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