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News:
Seeking Outreachy interns and project proposals
Bioconductor
Outreachy
community
3.0 years ago
Maria Doyle
▴ 110
1
vote
3
replies
1.5k
views
DESeq2 Installation Issue
DESeq2
updated 3.0 years ago by
Hervé Pagès
16k • written 3.0 years ago by
joanna
• 0
1
vote
1
reply
802
views
MSc student
genomes
updated 3.0 years ago by
Basti
▴ 780 • written 3.0 years ago by
Deeplaxmi
• 0
0
votes
1
reply
1.3k
views
RUV with K more than 1.
RUVSeq
updated 3.0 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
star
▴ 10
2
votes
4
replies
1.4k
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2
DifferentialExpression
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
idetoma
• 0
0
votes
1
reply
859
views
Rnaseq analysis using a continuous time series
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Aviads
• 0
0
votes
2
replies
1.8k
views
installing DESeq2 on Macbook R Studio
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Chatura
• 0
0
votes
1
reply
496
views
More information on results columns
DESeq2
updated 3.0 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
krigerkoalaen
• 0
1
vote
2
replies
5.0k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 3.0 years ago by
Gordon Smyth
53k • written 3.0 years ago by
Keith
• 0
3
votes
4
replies
2.4k
views
Processing data with voom "expression values" and "weights"
limma
voom
updated 3.0 years ago by
Gordon Smyth
53k • written 3.0 years ago by
Edmond
• 0
1
vote
1
reply
1.3k
views
how to call an app from Cytoscape using R?
RCy3
updated 3.0 years ago by
alex.pico
▴ 30 • written 3.0 years ago by
adR
▴ 40
0
votes
1
reply
904
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2
RNASeqData
DifferentialExpression
updated 3.0 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
Julie
• 0
4
votes
4
replies
2.7k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
Dario Strbenac
★ 1.6k
1
vote
3
replies
4.0k
views
Do the count values should be only integer to be able to use DESeq2?
DESeq2
3.0 years ago
Sep
• 0
0
votes
1
reply
1.0k
views
Updated package is not the version specified on the homepage
Versions
Update
BindingSiteFinder
updated 3.0 years ago by
Mike Smith
★ 6.6k • written 3.0 years ago by
M.Klostermann
• 0
0
votes
5
replies
1.6k
views
Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2
longitudinal
updated 3.0 years ago by
swbarnes2
★ 1.4k • written 3.0 years ago by
sharvari gujja
▴ 40
1
vote
3
replies
2.2k
views
Adding ellipse in PCAtools biplot
Biplot
FactoMineR
proteomics
PCAtools
ellipse
updated 3.0 years ago by
Kevin Blighe
★ 4.0k • written 3.0 years ago by
M Tuhin
• 0
3
votes
2
replies
1.1k
views
Help with the design matrix for longitudinal study
edgeR
3.0 years ago
sharvari gujja
▴ 40
1
vote
9
replies
2.4k
views
Is it possible to annotate a GRanges Object that has scaffolding names and not chromosome numbers?
Annotation
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
stacy.genovese
• 0
2
votes
4
replies
1.3k
views
Successor of genesBy Defunct Function
ensembldb
updated 3.0 years ago by
Hervé Pagès
16k • written 3.0 years ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
1.3k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 3.0 years ago by
Dario Strbenac
★ 1.6k • written 3.0 years ago by
Hicham
▴ 10
1
vote
2
replies
1.5k
views
select with org.Mm.eg.db does not give ENSEMBL ids
org.Mm.eg.db
3.0 years ago
raf4
▴ 30
4
votes
7
replies
1.9k
views
DESeq2: Repetitive padj values?
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
vanbelj
▴ 30
1
vote
1
reply
1.1k
views
Is this DESeq2 interactions design correct?
DESeq2
interactions
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
bhagyesh
• 0
0
votes
3
replies
1.4k
views
how to iterate all comparisons in group with "coef =" ?
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Theo
▴ 10
0
votes
8
replies
2.7k
views
DropletUtils::read10xCounts error
read10xCounts
DropletUtils
3.0 years ago
fdumetz
• 0
0
votes
3
replies
1.7k
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures
R
genomation
bed
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
sat
• 0
0
votes
2
replies
1.6k
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 3.0 years ago by
camilia.savitri
• 0
0
votes
2
replies
1.8k
views
Online Venn diagram generator where I can paste text files containing gene name lists to get the diagram
Venndiagram
files
text
3.0 years ago
ratto
• 0
2
votes
2
replies
816
views
Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
3.1 years ago • updated 3.0 years ago
SciencyUsagi
▴ 10
0
votes
1
reply
3.1k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Jayesh Kumar
• 0
0
votes
1
reply
1.2k
views
Help for RNA sequencing analysis with DESEQ2
DESeq2
star
differentiallyexpressed
updated 3.0 years ago by
Michael Love
43k • written 3.1 years ago by
nico
• 0
1
vote
3
replies
1.6k
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2
edgeR
rnaseqGene
updated 3.0 years ago by
Michael Love
43k • written 3.1 years ago by
vpl685
• 0
0
votes
1
reply
759
views
Combining VST counts for replicates
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Jayesh Kumar
• 0
0
votes
3
replies
2.9k
views
GSVA results interpretation
GSVA
updated 3.0 years ago by
Robert Castelo
★ 3.4k • written 3.0 years ago by
munta.jihad
• 0
0
votes
3
replies
1.5k
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb
AnnotationDbi
AnnotationForge
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
ahiser
• 0
0
votes
1
reply
1.7k
views
How to set threshold of padj value in DeSeq2
DESeq2
padj
default
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
Serena
• 0
3
votes
3
replies
7.2k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 3.0 years ago by
Gordon Smyth
53k • written 3.0 years ago by
Sara
• 0
5
votes
3
replies
3.0k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
3.3 years ago • updated 3.0 years ago
jamie.gearing
▴ 60
0
votes
2
replies
1.3k
views
Orange point meaning in plotSmear with edgeR
edgeR
plotSmear
3.0 years ago
Tess
• 0
0
votes
1
reply
844
views
Differential RNA seq on TCGA set
DESeq2
RNASeqData
updated 3.0 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
SilverCat
• 0
0
votes
2
replies
1.2k
views
microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene
microRNA
TxDb.Hsapiens.UCSC.hg38.knownGene
3.0 years ago
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
1.1k
views
Help needed to run PVCA
pvca
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
jyotsna.rao
• 0
0
votes
0
replies
1.0k
views
adding peptides to a multiple sequence alignment
msa
IRanges
Biostrings
3.0 years ago
Mario Dejung
• 0
0
votes
1
reply
490
views
rlog() transformation works only when using DESeqDataSet, not matrix
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
licheny
• 0
0
votes
7
replies
1.9k
views
Issue in generating a new DBA object with custom counts
DiffBind
dbaobject
3.1 years ago • updated 3.0 years ago
francesco.gandolfi
• 0
1
vote
0
replies
1.1k
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn
vsn
Normalization
vsn2
Proteomics
3.0 years ago
Arend
▴ 10
0
votes
1
reply
1.1k
views
Error in ATACseqQC bamQC analysis
ATACSeq
ATACseqQC
updated 3.0 years ago by
Ou, Jianhong
★ 1.3k • written 3.0 years ago by
tahir.msajid
• 0
0
votes
3
replies
1.5k
views
Gene TPM validity with STAR only quantification
RNASeq
written 3.1 years ago by
SciencyUsagi
▴ 10
0
votes
1
reply
1.4k
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 3.0 years ago by
alan.ocallaghan
▴ 160 • written 3.0 years ago by
cathalgking
▴ 10
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