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Views
Votes
0
votes
31
replies
4.4k
views
Error in find DEXSeq package
deseq
dexseq
9.0 years ago
engr.yahya602
• 0
1
vote
21
replies
5.2k
views
Warning: unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0
BiocManager
written 4.0 years ago by
Lucy
▴ 60
0
votes
21
replies
2.9k
views
How to use DECIPHER to design group-specific primers
Decipher
4.1 years ago
hoonhuiyi
• 0
34
votes
21
replies
14k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.7 years ago • updated 19 months ago
Michael Love
42k
0
votes
18
replies
5.9k
views
WGCNA error in network construction ?
microarray
rnaseq
7.2 years ago
m.azhar
▴ 10
0
votes
16
replies
3.2k
views
Rgraphviz installation fails
rgraphviz
6.8 years ago
Giovanni Calice
▴ 160
0
votes
16
replies
4.4k
views
Error while using buildindex for human genome
rsubread
buildindex
fasta
alignment
5.6 years ago
writetoroopali
• 0
4
votes
15
replies
6.2k
views
mzR installation error: "unable to load shared object"
mzR
installation
8.8 years ago
Eugene
• 0
0
votes
15
replies
2.8k
views
rlog not found
rlog
rlog transformation
6.0 years ago
crowsreign42
• 0
2
votes
15
replies
731
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 3 months ago by
Michael Love
42k • written 3 months ago by
cinzia.spagnoli
• 0
0
votes
14
replies
2.3k
views
Path to file in windows
bioconductor
R
windows
diffbind
updated 7.0 years ago by
Gord Brown
▴ 650 • written 7.1 years ago by
jorrenkuster
• 0
0
votes
14
replies
2.1k
views
Trouble downloading dada2
dada
dada2
15 months ago
elliottchon97
• 0
0
votes
14
replies
1.7k
views
Error while opening Mart with biomaRt package
software error
ensembl
biomart
4.4 years ago
loicborcard01
• 0
5
votes
13
replies
4.3k
views
Getting error
enrichplot
clusterProfiler
org.Hs.eg.db
updated 2.2 years ago by
793345316
▴ 40 • written 2.2 years ago by
beslinail
• 0
2
votes
13
replies
14k
views
Issues connecting with R 3.2.2 to source("http://bioconductor.org/biocLite.R")
spade
8.5 years ago
frostbite907
• 0
2
votes
13
replies
2.0k
views
Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6 first error: argu…
xcms
adjustRtime
parameters
scantime error
biocparallel error
4.7 years ago
abrsoule
▴ 30
2
votes
13
replies
481
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
27 days ago • updated 24 days ago
fernanda.backsouza
▴ 10
1
vote
12
replies
1.3k
views
Taking much longer time for same script after R upgrade to 4.0
R
3.9 years ago
hsiowa2
▴ 20
1
vote
12
replies
3.0k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 3.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.2 years ago by
naive
• 0
1
vote
12
replies
4.7k
views
WGCNA: correlations module-traits, and module membership-gene significance
WGCNA
co-expression analysis
gene significance
module membership
module-trait relationship
updated 23 months ago by
annamariabugaj
▴ 10 • written 4.7 years ago by
rodrigo.duarte88
▴ 30
1
vote
12
replies
3.9k
views
Problem with summarizeOverlaps function
genomicalignments
read counting
8.7 years ago
kgorczak
▴ 10
6
votes
12
replies
1.8k
views
Error when loading DMRcate
DMRcate
15 months ago
Bazingastats
• 0
0
votes
11
replies
4.4k
views
Examples from keggList in KEGGREST don't all work
software error
keggrest
8.2 years ago
Bryan Hanson
• 0
0
votes
11
replies
2.0k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq
ChIPSeqSpike
updated 3.3 years ago by
nicolas.descostes
• 0 • written 3.3 years ago by
Ainul
• 0
0
votes
11
replies
3.0k
views
Hello, I'm having trouble in installing Limma package and this is what Im getting
limma
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
Deepti
• 0
2
votes
11
replies
6.2k
views
biomaRT connexion problem make failed my unit tests
biomaRt
Peer's Certificate
Ensembl
updated 3.3 years ago by
Mike Smith
★ 6.5k • written 3.7 years ago by
ilysR
• 0
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.1 years ago • updated 2.0 years ago
Sarah_piggy
▴ 10
1
vote
11
replies
1.6k
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 12 months ago by
Martin Morgan
25k • written 12 months ago by
Michael Steinbaugh
▴ 90
5
votes
11
replies
2.8k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.6 years ago
khp
▴ 30
2
votes
11
replies
5.6k
views
Error: cannot allocate vector of size ...MB
limma
8.4 years ago
fahime.falahi
• 0
2
votes
11
replies
7.3k
views
ClusterProfiler enrichGO function leads to different enrichment results in different computers, while the code and gene list keep same
clusterProfiler
2.4 years ago
liuzhy
▴ 10
2
votes
11
replies
2.1k
views
RBGL installation error
rbgl
8.0 years ago
Julian Gehring
★ 1.3k
0
votes
11
replies
2.2k
views
rsbml fails to compile on Linux due to ParseMessage.h undetected with libSBML 5
rsbml
compilation error
configure
7.4 years ago
zeb
• 0
14
votes
10
replies
3.7k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.5 years ago
Deleted
▴ 70
1
vote
10
replies
2.7k
views
Building mzR package under docker fails
mzR
docker
debian
centos
rocker
8.6 years ago
mjmg
• 0
2
votes
10
replies
6.1k
views
Install older specific version from an R package that is on the Bioconductor Repository
Bioconductor
biocLite
R packages
oldversion
8.5 years ago
svlachavas
▴ 830
2
votes
10
replies
2.2k
views
DEseq normalization Small RNA-seq data using rRNA
deseq2
normalization
smallrna
ribosomal rna
7.6 years ago
mosharrofgeb
▴ 10
2
votes
10
replies
1.2k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago
rohitsatyam102
▴ 20
0
votes
10
replies
1.9k
views
Phyloseq to metagenomeSeq
limma
metagenomeSeq
5.0 years ago
Jitendra
▴ 10
0
votes
10
replies
2.0k
views
behaviour of findOverlaps on GRangesList object
findOverlaps
grangeslist
GenomicRanges
6.9 years ago
lovro0
▴ 10
0
votes
10
replies
2.0k
views
Ability to use a particular package via Docker
Docker
flowcore
dockerfile
7.7 years ago
jordan.xanthopoulos
• 0
0
votes
9
replies
1.8k
views
Volcano plot non-numeric argument error
volcano plot
edgr
7.3 years ago
elena.capel
▴ 10
0
votes
9
replies
1.5k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps
R
GenomicAlignments
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
cavery
• 0
3
votes
9
replies
2.9k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles
AnnotationForge
Bimap
GO
9.7 years ago
artur
▴ 80
4
votes
9
replies
7.9k
views
Upper triangular matrix heatmap using pheatmap package
pheatmap
8.4 years ago
Deepak Tanwar
▴ 10
0
votes
9
replies
1.3k
views
invalid class “NormalyzerEvaluationResults” object: invalid object for slot "lowVarFeaturesCVs" in class "NormalyzerEvaluationResults": got class "NU…
NormalyzerDE
updated 2.1 years ago by
Jakob Willforss
• 0 • written 2.2 years ago by
Alejandro
• 0
0
votes
9
replies
2.6k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
5.5 years ago
A
▴ 40
0
votes
9
replies
1.4k
views
AnnotationHub: failed to load resource name
DFP
2.9 years ago
hxwanghxw
• 0
1
vote
9
replies
3.0k
views
Dotplots for differential gene expression data ?
clusterprofiler
3.9 years ago
sunnykevin97
• 0
7
votes
9
replies
1.7k
views
codelink package is not installing
codelink
r
9.1 years ago
Agaz Hussain Wani
▴ 260
1,000 results • Page
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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