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Votes
4
votes
6
replies
2.1k
views
Speedglm dependency issue?
nullranges
2.6 years ago
Kathleen Reed
▴ 20
0
votes
1
reply
1.0k
views
Can't make a boxplot or hist with oligo
oligo
updated 2.6 years ago by
James W. MacDonald
68k • written 2.7 years ago by
i.am.filippov
• 0
1
vote
2
replies
1.4k
views
Error in getCdfInfo(object) :
MicroarrayData
2.6 years ago
kobra
• 0
0
votes
0
replies
716
views
Cannot generate plots when calling ChAMP
ChAMP
DMP.GUI
2.6 years ago
Kan
• 0
0
votes
0
replies
602
views
Gene A mutation vs Gene B amplification using TCGA datasets
TCGAWorkflow
2.6 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
2.6 years ago
vk
• 0
0
votes
0
replies
847
views
Reading FCS files using read.FCS
read.FCS
read.flowSet
2.7 years ago
Pilid
• 0
0
votes
1
reply
764
views
Sample expression calculation in rna seq
Rnaseq
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
zaid ur
• 0
0
votes
0
replies
856
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
3.0k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
2.7 years ago • updated 2.6 years ago
Chris
▴ 20
2
votes
3
replies
1.5k
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 2.6 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
1.2k
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 • updated 2.6 years ago
neilzhao
▴ 30
0
votes
1
reply
868
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
1.5k
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
939
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
851
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
970
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
3.6k
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
1.7k
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
5.3k
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
564
views
Package requires binary executable from external software?
external
executable
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
t.m.jarva13
• 0
0
votes
0
replies
822
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
776
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 • updated 2.6 years ago
Weiqian
▴ 10
2
votes
2
replies
931
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
2.4k
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
1.5k
views
GSVA with and without absolute scaling method
GSVA
2.7 years ago
arashdeep singh
• 0
0
votes
1
reply
971
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 • updated 2.6 years ago
epipally
• 0
2
votes
8
replies
4.4k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
2.7 years ago • updated 2.5 years ago
Luis
• 0
0
votes
2
replies
1.6k
views
ModuleExprScore function/ hdWGNCA
ModuleExprScore
DotPlot
hdWGNCA
Seurat
2.7 years ago
Yuko
• 0
0
votes
0
replies
864
views
News:
Bioconductor Release 3.16 Code Freeze
release
Release
Bioconductor
2.7 years ago
shepherl
4.2k
0
votes
1
reply
1.1k
views
Mapping of probe IDs to gene gene symbols for Affymetrix Human Clariom D Assay platform
GeneMapping
AnnotationDbi
AffymetrixDataTestFiles
GeneExpressionSignature
org.Hs.eg.db
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Prachi
• 0
4
votes
2
replies
3.8k
views
Normalisation of data using DESeq2 with multi-groups
DEseq2
2.7 years ago
Changsuk
▴ 10
0
votes
2
replies
824
views
DESeq2 design matrix accounting for high heterogeneity of individuals inside a group
DESeq2
2.7 years ago
a.wag
• 0
2
votes
2
replies
1.2k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
2.7 years ago
Abdul
▴ 20
1
vote
1
reply
920
views
Can I run deseq2 on two separate experiments at once?
rnaseq
deseq2
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
lunarskye222
• 0
46,691 results • Page
55 of 934
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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