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2
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7
replies
4.8k
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Installing Local packages in Bioconductor
package
updated 9 months ago by
Boxun
• 0 • written 2.0 years ago by
BioC123
• 0
3
votes
3
replies
4.8k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 11 months ago by
Guido Hooiveld
★ 4.0k • written 4.1 years ago by
t.b.kuipers
• 0
1
vote
5
replies
4.8k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 10 months ago by
Yang Liao
▴ 380 • written 2.9 years ago by
s.muroy
▴ 10
1
vote
7
replies
4.6k
views
Problems Installing biomaRt
biomaRt
updated 6 months ago by
James W. MacDonald
66k • written 2.1 years ago by
ksci
▴ 20
2
votes
28
replies
4.5k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 5 months ago by
James W. MacDonald
66k • written 17 months ago by
Manmohit
▴ 10
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 12 months ago by
IUH
• 0 • written 6.9 years ago by
stan
• 0
0
votes
3
replies
4.4k
views
The MicrobiotaProcess package performed lefse analysis and had a problem drawing the tree
MicrobiotaProcess
offspring.tbl_tree_item
updated 10 months ago by
Itscontentstop
• 0 • written 10 months ago by
fengjieli2021
• 0
7
votes
6
replies
4.3k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 7 months ago by
Marcel Ramos
700 • written 21 months ago by
Recep
▴ 20
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by
seeker
• 0
2
votes
2
replies
4.2k
views
choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation
rlog transformation
deseq2
updated 6 months ago by
Alessandro Silvestris
• 0 • written 6.4 years ago by
lirongrossmann
▴ 80
6
votes
5
replies
4.2k
views
DESeq2: Extremely low pvalues
deseq2
updated 10 months ago by
James W. MacDonald
66k • written 7.8 years ago by
szenitha
▴ 20
6
votes
11
replies
4.1k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 10 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
2
votes
2
replies
4.0k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 10 months ago by
Trinh
• 0 • written 7.9 years ago by
mdtorohernando
▴ 10
5
votes
8
replies
4.0k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
10
votes
8
replies
4.0k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by
Mingkee
• 0 • written 6.9 years ago by
yura.grabovska
▴ 30
5
votes
6
replies
3.9k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 3 months ago by
briankleiboeker
• 0 • written 3.2 years ago by
r.i.s.alnuwaysir
▴ 10
0
votes
11
replies
3.8k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 3 months ago by
Tim Peters
▴ 180 • written 7.2 years ago by
Jenny Drnevich
★ 2.0k
0
votes
5
replies
3.8k
views
PCA plot for TPM data
PCA
written 6.6 years ago by
tanyabioinfo
▴ 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
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 8 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 3 months ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
0
votes
1
reply
3.7k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
updated 8 months ago by
James W. MacDonald
66k • written 8 months ago by
Aytaç
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 15 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
1
vote
11
replies
3.7k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by
Manuel
• 0 • written 10 months ago by
Elham
• 0
0
votes
4
replies
3.7k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 11 months ago by
Marco
• 0 • written 4.5 years ago by
mathai.c
• 0
1
vote
4
replies
3.6k
views
ggtree functions suddenly stopped working: "Error in offspring.tbl_tree_item(..."
ggtree
updated 10 months ago by
xushuangbin
• 0 • written 10 months ago by
Hank
• 0
0
votes
2
replies
3.6k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.8 years ago by
ag1805x
▴ 80
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 4 months ago by
YNPAN910
• 0 • written 4.8 years ago by
maya.kappil
▴ 30
4
votes
4
replies
3.5k
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
written 3.2 years ago by
changxu.fan
▴ 20
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 11 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
0
votes
3
replies
3.5k
views
ASpli: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'sort': 'start' or 'end' canno…
ASpli
updated 8 months ago by
andresrabinovich
• 0 • written 19 months ago by
thithusuong.nguyen
• 0
1
vote
16
replies
3.4k
views
error in ChAMP loading file
ChAMP
updated 10 weeks ago by
hortense96
• 0 • written 18 months ago by
Giulia
• 0
1
vote
3
replies
3.4k
views
SRAdb: Error downloading sqlite files
sradb
written 6.6 years ago by
arielle
• 0
2
votes
10
replies
3.3k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 7 months ago by
Michael Love
42k • written 5.8 years ago by
andrebolerbarros
▴ 20
0
votes
5
replies
3.3k
views
diffbind
DiffBind
chipseq
updated 10 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
ANAMIKA
• 0
1
vote
2
replies
3.3k
views
Extract genes from ggvenn?
ggvenn
updated 6 weeks ago by
Michael
▴ 10 • written 2.1 years ago by
axe880
• 0
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO
clusterProfiler
written 3.3 years ago by
Carolina
• 0
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges
genomicfeatures
translation
updated 4 months ago by
russ.bainer
▴ 10 • written 8.5 years ago by
madsheilskov
▴ 10
2
votes
9
replies
3.2k
views
NCBI Locus ID to gene ID conversion
LocusIDtogeneIDconversion
updated 6 months ago by
IP
• 0 • written 20 months ago by
KMS
▴ 20
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 12 months ago by
Sabiha
▴ 20
0
votes
4
replies
3.2k
views
Problems with FLOWAI
flowAI
written 3.1 years ago by
msoares
• 0
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 7 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
9
replies
3.2k
views
clarification about bumphunter value output
minfi
bumphunter
updated 12 months ago by
Jennifer Dehner
• 0 • written 6.2 years ago by
src3
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 7 weeks ago by
Gordon Smyth
50k • written 9.9 years ago by
Arvid Sondén
▴ 40
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 6 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
2
votes
3
replies
3.1k
views
Filtering low intensity probes in microarray data
Hugene1.0 ST
written 6.8 years ago by
pbachali
▴ 50
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 9 weeks ago by
snijesh
▴ 20 • written 6.6 years ago by
Ramiro Magno
▴ 100
16
votes
25
replies
3.1k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 10 months ago by
adi.rotem
• 0 • written 8.1 years ago by
dsg16
▴ 20
1
vote
9
replies
3.0k
views
DEGreport installation help
DEGreport
updated 8 months ago by
James W. MacDonald
66k • written 20 months ago by
marinaw
▴ 20
1,748 results • Page
2 of 35
Recent ...
Replies
Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Comment: slingshot: error with plot3d.SlingshotDataSet
by
Happiness
• 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
mohammedtoufiq91
▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Votes
Answer: recount3 problem downloading data from source sra
Answer: recount3 problem downloading data from source sra
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
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