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4
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Problem with pd.hta.2.0 package installation
Install
1 hour ago
croft.carys
• 0
0
votes
2
replies
177
views
News:
List of Deprecated Packages for Bioc3.13
Deprecation
Workflow
Software
ExperimentData
3 months ago • updated 3 hours ago
shepherl
2.5k
0
votes
1
reply
22
views
DESeq2 calling DEGs despite detection in few replicates
DESeq2
3 hours ago
lnblock2
• 0
• updated 3 hours ago
swbarnes2
• 650
0
votes
3
replies
65
views
AnnotationForge: makeOrgPackageFromNCBI Error in function (type, msg, asError = TRUE) : FTP response timeout
AnnotationForge
2 days ago
Imad
• 0
• updated 2 hours ago
Kevin Blighe
2.5k
2
votes
1
reply
48
views
Geno Ontology Analysis using gene symbol
GO.db
Annotation
Clusterprofile
GeneOntology
15 hours ago
MOHAMMAD
• 0
• updated 7 hours ago
bastien.ducreux
• 20
0
votes
0
replies
21
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
9 hours ago
Enrico
• 0
0
votes
0
replies
17
views
Gene network orientation grndata
grndata
10 hours ago
stijn.hawinkel
• 0
1
vote
3
replies
37
views
Getting number of datasets with flowCore
flowCore
11 hours ago
mark.holmes
• 0
• updated 4 hours ago
SamGG
• 270
0
votes
3
replies
48
views
add group info within DGE-object before TMM normalization
edgeR
limma
14 hours ago
R
• 40
• updated 8 minutes ago
Gordon Smyth
42k
0
votes
1
reply
39
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
2 days ago
Angel
• 0
• updated 13 hours ago
Alejandro Reyes
♦ 1.7k
0
votes
3
replies
50
views
How to calculate coefficient of variation within group?
edgeR
limma
RNASeqPower
19 hours ago
Ahdee
• 50
• updated 50 minutes ago
Gordon Smyth
42k
0
votes
0
replies
19
views
How to increase the number of primer set output in openPrimeR
openPrimeR
1 day ago
marongiu.luigi
• 0
0
votes
2
replies
83
views
DESeq2 design formula and batch correction
DESeq2
2 days ago
lransom
• 0
• updated 1 day ago
Michael Love
32k
0
votes
3
replies
82
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
2 days ago
sp
• 0
• updated 1 day ago
Michael Love
32k
0
votes
1
reply
18
views
Error installing diffuStats: compilation failed
diffuStats
1 day ago
sergi.picart
• 20
0
votes
0
replies
35
views
How to know the number of detected CpG islands with RnBeads
RnBeads
1 day ago
Federica
• 10
0
votes
1
reply
39
views
How to save primers in local file in openPrimeR
openPrimeR
1 day ago
marongiu.luigi
• 0
1
vote
2
replies
96
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
2 days ago • updated 1 day ago
Lucky
• 0
0
votes
1
reply
44
views
Error in UseMethod("filter_") for RIPSeeker package
biomaRt
Bioconductor-RIPSeeker
2 days ago
Yongqing
• 0
• updated 2 days ago
Mike Smith
♦ 4.9k
1
vote
2
replies
76
views
fgsea usage question - what gene set to use?
fgsea
2 days ago • updated 13 hours ago
alexandr.gopanenko
• 20
1
vote
1
reply
62
views
read nanopore Fastq file
NanoporeRNASeq
RNASeq
3 days ago
sinanoori88
• 0
• updated 2 days ago
James W. MacDonald
56k
2
votes
3
replies
98
views
error when reading fastq file
FastqCleaner
fastq
ShortRead
4 days ago
sinanoori88
• 0
• updated 3 days ago
James W. MacDonald
56k
1
vote
1
reply
73
views
News:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview
pathways
SBGNview.data
pathview
visualization
5 days ago • updated 3 days ago
Luo Weijun
♦ 1.5k
0
votes
1
reply
35
views
topGo GenTable returns result column as character
GenTable
topGO
3 days ago
dario.beraldi
• 0
• updated 3 days ago
James W. MacDonald
56k
0
votes
0
replies
29
views
stageR error - Some genes have only one transcript; this is incompatible with DTU correction. Remove these transcripts.
stageR
DRIMSeq
3 days ago
sbcn
• 60
1
vote
4
replies
127
views
ribosomeProfilingQC - countReads function - is it possible to consider library type - non-stranded, forward-stranded or rev-stransded?
ribosomeProfilingQC
countReads
8 days ago • updated 2 days ago
alexandr.gopanenko
• 20
0
votes
1
reply
55
views
iupac2meme function missing in universalmotif package
universalmotif
11 days ago
lessismore
• 0
• updated 3 days ago
b2tremblay
• 0
1
vote
1
reply
84
views
An attempt to better understand DESeq2 dispersion estimation
DESeq2
4 days ago
Sam
• 10
• updated 3 days ago
Michael Love
32k
0
votes
1
reply
82
views
Biological replicates in DESeq2
DESeq2
Bioconductor
RNASeqR
4 days ago
Blanca
• 0
• updated 3 days ago
ATpoint
• 480
3
votes
1
reply
46
views
How to find rsID with biomaRt in R
biomaRt
3 days ago
Federica
• 10
• updated 3 days ago
Mike Smith
♦ 4.9k
1
vote
4
replies
84
views
Issues with setting up `rJava` in Github actions for package checking
github-actions
biocthis
rJava
3 days ago
aravind-j
• 20
2
votes
2
replies
81
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
4 days ago
Jason
• 0
• updated 3 days ago
Yang Liao
• 220
0
votes
17
replies
205
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
5 days ago
lea
• 0
• updated 4 days ago
James W. MacDonald
56k
0
votes
1
reply
69
views
tximport rowsum error
tximport
7 days ago • updated 4 days ago
Ezgi
• 30
0
votes
0
replies
40
views
News:
Submission Deadline for Bioc2021 Next Week!
Conference
Bioc2021
4 days ago
shepherl
2.5k
0
votes
0
replies
55
views
Job:
Bioinformatician in Core Facility (100%)
JobPosting
Job
Switzerland
Basel
4 days ago
Robert Ivanek
• 660
0
votes
0
replies
37
views
Job:
Bioinformatician at MiroBio, Oxford, UK
Transcriptomics
Bioconductor
Statistics
Job
Biocon
4 days ago
m.jackson
• 0
0
votes
0
replies
37
views
metage problem with DESeq
DESeq
metagene2
metagene
4 days ago
GM
• 10
1
vote
3
replies
123
views
Batch correction and DESeq2
DESeq2
6 days ago • updated 4 days ago
Alessia
• 0
0
votes
0
replies
57
views
VCF File too large for tabix. Best option to make it usable with R?
samtools
tabix
VariantAnnotation
VCFArray
4 days ago
naive
• 0
1
vote
2
replies
69
views
Diffbind error while running example data
DiffBind
5 days ago • updated 4 days ago
Lucky
• 0
1
vote
3
replies
96
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
6 days ago • updated 5 days ago
changxu.fan
• 0
0
votes
0
replies
36
views
How to get illumina CpG IDs by gene name?
MethylationArrayData
RnBeads
5 days ago
D
• 0
0
votes
1
reply
61
views
Can you colour dendrogram branch clusters in pheatmap?
R
heatmaps
pheatmap
6 days ago
trichorico
• 10
• updated 5 days ago
Kevin Blighe
2.5k
2
votes
1
reply
68
views
Splitting multiple groups - three different ages
DESeq2
5 days ago
jd348
• 0
• updated 5 days ago
Michael Love
32k
0
votes
3
replies
112
views
Same methylation probe ID with different locus annotations in Illumina 27k and 450k plotforms
IlluminaHumanMethylation27kanno.ilmn12.hg19
5 days ago
yuabrahamliu
• 0
• updated 2 days ago
Kevin Blighe
2.5k
0
votes
1
reply
50
views
DESeq2, tximport normalization, normalization factors, size factors
tximport
DESeq2
normalizationfactors
sizefactors
5 days ago
svenbioinf
• 0
• updated 5 days ago
Michael Love
32k
2
votes
4
replies
87
views
Removing rows (countData) from a DESeq Object
DESeq2
5 days ago
Bine
• 0
3
votes
1
reply
63
views
Using group instead of interaction term on a custom edited matrix
DESeq2
6 days ago
jd348
• 0
• updated 5 days ago
Michael Love
32k
1
vote
2
replies
93
views
DMRcate extractRanges error
DMRcate
6 days ago • updated 3 days ago
macsue.jacques
• 10
40,319 results • Page
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Comment: add group info within DGE-object before TMM normalization
by
Gordon Smyth
42k
Your questions are answered by the documentation. You need to include the design matrix both for voom and for the fitting linear models. Th…
Comment: How to calculate coefficient of variation within group?
by
Gordon Smyth
42k
My advise to choosing a log fold cutoff is not to use one. I have said many times, including in my answer above, that fold change cutoffs s…
Comment: How to calculate coefficient of variation within group?
by
Ahdee
• 50
Thanks Gordon for the estimateCommonDisp. I see your point. However what I want to do was to do post lookback to see if a certain effectiv…
Answer: DESeq2 calling DEGs despite detection in few replicates
by
swbarnes2
• 650
The software is correctly detecting a difference in averages between the two groups. It's really not the software's place to be deciding i…
Comment: Getting number of datasets with flowCore
by
SamGG
• 270
Great job! Thanks for sharing.
Votes
A: Did not find function «.rowMeans»
Answer: Geno Ontology Analysis using gene symbol
Answer: Geno Ontology Analysis using gene symbol
A: Struggling with use and interpretation of "Group-specific condition effects, ind
Comment: Getting number of datasets with flowCore
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