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1
vote
2
replies
1.3k
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
akrunic
• 0
0
votes
3
replies
2.8k
views
getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
written 2.7 years ago by
nhaus
▴ 70
0
votes
1
reply
750
views
Time change in expression vs time change in phenotype
Transcriptomics
ExpressionData
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Ivan
• 0
0
votes
1
reply
1.2k
views
Unable to create pd file for ChAMP analysis
ChAMP
updated 18 months ago by
tahirah.yasmin2014
• 0 • written 2.7 years ago by
Monalisa
• 0
1
vote
0
replies
918
views
Make custom Txdb class objects from Txdb
GenomicFeatures
karyoploteR
TxDb.Hsapiens.UCSC.hg19.knownGene
2.7 years ago
Shreyash
▴ 10
1
vote
3
replies
1.4k
views
fc value in ggmaplot does not correspond to the real lfc value on the plot
DESeq2
ggmaplot
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
LEGO
• 0
3
votes
12
replies
3.0k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
urwah
▴ 10
0
votes
1
reply
1.1k
views
scRNAseq Download Errors
scRNAseq
updated 2.7 years ago by
shepherl
4.2k • written 2.7 years ago by
Dario Strbenac
★ 1.6k
4
votes
6
replies
2.1k
views
Speedglm dependency issue?
nullranges
2.7 years ago
Kathleen Reed
▴ 20
0
votes
1
reply
1.0k
views
Can't make a boxplot or hist with oligo
oligo
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
i.am.filippov
• 0
1
vote
2
replies
1.5k
views
Error in getCdfInfo(object) :
MicroarrayData
2.7 years ago
kobra
• 0
0
votes
0
replies
719
views
Cannot generate plots when calling ChAMP
ChAMP
DMP.GUI
2.7 years ago
Kan
• 0
0
votes
0
replies
605
views
Gene A mutation vs Gene B amplification using TCGA datasets
TCGAWorkflow
2.7 years ago
Begin-R
• 0
2
votes
4
replies
2.6k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
2.7 years ago
vk
• 0
0
votes
0
replies
858
views
Reading FCS files using read.FCS
read.FCS
read.flowSet
2.7 years ago
Pilid
• 0
0
votes
1
reply
773
views
Sample expression calculation in rna seq
Rnaseq
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
zaid ur
• 0
0
votes
0
replies
861
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
2.7 years ago
Priya
• 0
9
votes
16
replies
3.1k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
2.7 years ago
Chris
▴ 20
2
votes
3
replies
1.6k
views
Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma
CustomCDF
Affyhgu133aExpr
limma
affy
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Pratik Mehta
▴ 10
0
votes
2
replies
1.3k
views
error in champ.SVD
svd
methylation
champ
updated 2.7 years ago by
shepherl
4.2k • written 2.7 years ago by
Giulia
• 0
2
votes
2
replies
1.8k
views
Error in checkFullRank(modelMatrix)
DESeq2
BatchEffect
DifferentialExpression
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
AZ
▴ 30
1
vote
2
replies
1.8k
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
2.7 years ago
Abdul
▴ 20
1
vote
1
reply
3.2k
views
FPKM t-test vs DEseq2
DESeq2
statistics
rna-seq
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
SH
▴ 10
0
votes
1
reply
1.3k
views
EGSEA::egsea - Parallelization issue and "Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : negative length vectors are not allowed"
egsea
EGSEA123
2.7 years ago
neilzhao
▴ 30
0
votes
1
reply
872
views
Can I use baseMean (from DESeq2) as part of presenting/ interpreting results
DESeq2
diferentialabundance
16srRNA
baseMean
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
PhD_student_microbiome
• 0
0
votes
4
replies
1.0k
views
Down weighing an outlier in DESeq2 ?
DESeq2
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
Sydney
• 0
0
votes
0
replies
1.3k
views
Job:
Bioinformatics postdoc position at Penn State University
postdoc
Computational
Bioinformatics
Biology
Genomics
2.7 years ago
yuzun
• 0
0
votes
2
replies
1.6k
views
How to find the number of protein-coding genes in each chromosome arm in human?
gene
chromosome
proteincodinggene
2.7 years ago
Liliian
• 0
0
votes
0
replies
948
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
2.7 years ago
aymanreffai
• 0
2
votes
0
replies
2.6k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
2.7 years ago
Tadeoye
▴ 20
1
vote
1
reply
858
views
Performing a one-sided test for differential expression analysis in edgeR
edgeR
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
f_rahmdani
• 0
0
votes
0
replies
979
views
Manually adjusting BCV for exactTest in edgeR based on plotBCV
edgeR
2.7 years ago
f_rahmdani
• 0
1
vote
1
reply
3.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 2.7 years ago by
Guido Hooiveld
★ 4.1k • written 2.7 years ago by
morgan.sobol
▴ 10
4
votes
5
replies
3.7k
views
EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics
EnhancedVolcano
updated 2.7 years ago by
Kevin Blighe
★ 4.0k • written 2.7 years ago by
Peter
▴ 20
0
votes
4
replies
1.8k
views
Unable to install BiocManager
Biocmanager
R
updated 2.7 years ago by
L
▴ 50 • written 2.7 years ago by
sidrah19220
• 0
6
votes
6
replies
5.5k
views
DESeq2 for single cell pseudobulk processing
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.7 years ago by
r2626
▴ 10
0
votes
1
reply
573
views
Package requires binary executable from external software?
external
executable
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
t.m.jarva13
• 0
0
votes
0
replies
829
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
2.7 years ago
barrypraveen
• 0
0
votes
1
reply
780
views
Differential express genes in one group across all time points
DESeq2
edgeR
BP4RNAseq
ensemblVEP
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
DHARMESH
• 0
4
votes
5
replies
2.3k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 18 months ago by
ij283
• 0 • written 2.7 years ago by
Bernardo
▴ 10
0
votes
3
replies
1.7k
views
Differential Expression Analysis between Clusters
DESeq2
updated 2.7 years ago by
happytailor359
• 0 • written 2.7 years ago by
hoya1915
• 0
5
votes
5
replies
4.7k
views
How to combine two DESeq2 objects (dds) for analysis
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Luke
▴ 10
1
vote
5
replies
2.9k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
2.7 years ago
Weiqian
▴ 10
2
votes
2
replies
939
views
How Can I Assess the Reliability of BCV (Square-Root Dispersion) in Non-Replicated Experiments for Differential Expression Analysis Using edgeR?
edgeR
2.7 years ago
f_rahmdani
• 0
1
vote
2
replies
1.5k
views
Removing Unwanted Variations
DESeq2
NanoStringNCTools
RUVnormalize
RUVSeq
DifferentialExpression
2.7 years ago
AZ
▴ 30
1
vote
3
replies
1.3k
views
Recount3 data correspond to TCGA data
recount3
updated 10 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.7 years ago by
kevin lee
• 0
0
votes
1
reply
2.5k
views
biomaRt - NameSpace loading failed
biomaRt
bioma
updated 2.7 years ago by
Mike Smith
★ 6.6k • written 2.7 years ago by
Alessia
• 0
0
votes
2
replies
1.6k
views
GSVA with and without absolute scaling method
GSVA
2.7 years ago
arashdeep singh
• 0
0
votes
1
reply
978
views
Plotting read densities from DiffBind results
Read
density
DiffBind
updated 2.7 years ago by
Rory Stark
★ 5.2k • written 2.7 years ago by
bhandary.8590
▴ 20
0
votes
2
replies
1.2k
views
Question regarding multiple comparisons in DiffBind
DiffBind
2.7 years ago
epipally
• 0
46,699 results • Page
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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…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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