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News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
8 days ago
shepherl
3.9k
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 0
4
votes
12
replies
990
views
Ensembl down???
biomaRt
5 months ago
bas_work
▴ 30
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges
genomicfeatures
translation
updated 3 months ago by
russ.bainer
▴ 10 • written 8.4 years ago by
madsheilskov
▴ 10
4
votes
6
replies
760
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
3 months ago
isaac.vock
• 0
4
votes
2
replies
644
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago
Habil Zare
▴ 200
4
votes
6
replies
2.3k
views
DESeq2 for single cell pseudobulk processing
DESeq2
updated 12 months ago by
Michael Love
42k • written 13 months ago by
r2626
• 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago • updated 3 months ago
Luca
• 0
4
votes
2
replies
572
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
7 days ago • updated 3 days ago
gene_bioconductor
▴ 10
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 3.5 years ago by
ATpoint
★ 4.1k
4
votes
9
replies
1.3k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 8 months ago by
dbunis
▴ 10 • written 8 months ago by
nina.hahn
▴ 10
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 7 months ago by
Michael Love
42k • written 8 months ago by
Christian
• 0
4
votes
4
replies
1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 8 weeks ago by
feather-W
• 0 • written 13 months ago by
Bernardo
▴ 10
4
votes
4
replies
3.4k
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
written 3.2 years ago by
changxu.fan
▴ 20
4
votes
6
replies
682
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 8 weeks ago by
Akshay
• 0 • written 5 months ago by
Sarah
▴ 10
4
votes
7
replies
880
views
weird volcano plot
DESeq2
updated 9 weeks ago by
Shuning
• 0 • written 6 months ago by
shouzheng
▴ 10
4
votes
2
replies
1.1k
views
metagene: paired-end bam as input
metagene
updated 6 months ago by
xlal
• 0 • written 7.6 years ago by
anton.kratz
▴ 60
4
votes
3
replies
345
views
Bioconductor code browser time out
Bioconductor
updated 4 months ago by
Mike Smith
★ 6.5k • written 4 months ago by
Marek Gierlinski
▴ 30
4
votes
4
replies
1.7k
views
biomaRt error: database disk image is malformed
biomaRt
updated 11 months ago by
Emile
• 0 • written 2.6 years ago by
victorcampos1995
▴ 10
4
votes
3
replies
965
views
WGCNA documentation not available
WGCNA
written 5 months ago by
ramonmassoni
▴ 10
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive
bioconductor
updated 6 months ago by
shepherl
3.9k • written 19 months ago by
Florian Finkernagel
▴ 30
4
votes
4
replies
832
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
4
votes
12
replies
3.8k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 7 months ago by
Miguel
• 0 • written 3.2 years ago by
robert.chen
• 0
4
votes
5
replies
877
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 7 months ago by
Gordon Smyth
50k • written 8 months ago by
Jonathan
▴ 10
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
garcia
• 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
4
votes
2
replies
1.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Jonathan
▴ 10
4
votes
6
replies
445
views
FilterByExpr low counts with small sample size
edgeR
22 days ago • updated 17 days ago
Jonathan
▴ 10
4
votes
4
replies
440
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Geo
• 0
4
votes
6
replies
612
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
4
votes
5
replies
2.0k
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 7 months ago by
jacorvar
▴ 40 • written 19 months ago by
eraldagjika
▴ 20
4
votes
3
replies
365
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 7 weeks ago by
Shaimaa Gamal
• 0 • written 9.0 years ago by
Pauly Lin
▴ 150
4
votes
7
replies
1.0k
views
Fishpond/Swish Interaction Test Error
fishpond
swish
10 months ago
Miguel
▴ 20
4
votes
9
replies
441
views
Memory errors using read.bismark?
dmrseq
bsseq
29 days ago • updated 2 days ago
Juan Higareda
• 0
4
votes
3
replies
239
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 7 weeks ago by
Georg
• 0
4
votes
13
replies
1.8k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
updated 7 months ago by
Hervé Pagès
16k • written 2.6 years ago by
Koki
▴ 10
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 7 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
4
votes
2
replies
372
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 3 months ago by
sansan
• 0
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 11 months ago by
IUH
• 0 • written 6.9 years ago by
stan
• 0
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 5 months ago by
Gordon Smyth
50k • written 2.4 years ago by
mohammedtoufiq91
▴ 10
4
votes
4
replies
1.2k
views
S4Vectors masking utils::findMatches is returning warnings in R 4.3 / Bioconductor 3.17
S4Vectors
written 12 months ago by
Michael Steinbaugh
▴ 90
4
votes
7
replies
717
views
DESeq2 unable to handle large count values
DESeq2
updated 7 weeks ago by
Michael Love
42k • written 6 months ago by
robennet
• 0
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 4 months ago by
YNPAN910
• 0 • written 4.7 years ago by
maya.kappil
▴ 30
4
votes
11
replies
2.6k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 11 months ago by
Aung
• 0 • written 14 months ago by
pedro-marra
▴ 10
3
votes
4
replies
235
views
Help with error using camera() in limma
CAMERA
limma
9 days ago
Chris
• 0
3
votes
5
replies
640
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 9 weeks ago by
Michael Love
42k • written 10 weeks ago by
sap275
▴ 10
3
votes
4
replies
542
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
1,745 results • Page
3 of 35
Recent ...
Replies
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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