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0
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5
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8.4k
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Pheatmap/Complexheatmap: making a continuous color scale with NAs
R
Pathways
pheatmap
limma
written 4.9 years ago by
Ridha
▴ 10
0
votes
6
replies
8.2k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
deseq2
R
genomics
8.1 years ago
mokunf
• 0
3
votes
3
replies
8.1k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 2.7 years ago by
Guido Hooiveld
★ 4.1k • written 5.8 years ago by
t.b.kuipers
• 0
5
votes
14
replies
7.9k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R
deseq2
edger
differential gene expression
fold change
updated 3.8 years ago by
ATpoint
★ 5.0k • written 7.6 years ago by
Beginner
▴ 60
6
votes
3
replies
7.6k
views
Heatmap Plotting in R
heatmap
R
bioconductor
10.6 years ago • updated 8.9 years ago
Deepak Tanwar
▴ 10
0
votes
5
replies
7.6k
views
Blastp - through R
blast
R
10.1 years ago
maahpishanu
• 0
2
votes
2
replies
7.5k
views
R 3.2.0 problem with DESeq2 - Hmisc error
deseq2
r
software error
updated 10.8 years ago by
Steve Lianoglou
★ 13k • written 10.8 years ago by
rclaire
▴ 20
1
vote
8
replies
7.5k
views
Cannot read Biom file
r
biomformat
phyloseq
updated 8.3 years ago by
Axel Klenk
★ 1.1k • written 8.3 years ago by
channen1221
• 0
1
vote
2
replies
7.5k
views
explanation of makeContrasts function of limma package
limma
microarray
R
geneexpression
updated 10.6 years ago by
Aaron Lun
★ 29k • written 10.6 years ago by
elisa.micarelli
▴ 10
3
votes
5
replies
7.4k
views
Tutorial:
Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R
GEO
geoquery
geoquery error message
Tutorial
8.1 years ago
martinguerrerog89
▴ 20
3
votes
4
replies
7.4k
views
Subset GRanges object into new object
R
genomicranges
subsetting
8.3 years ago
jhanks1981
• 0
4
votes
5
replies
7.4k
views
Up/Down Regulated GeneList from edgeR and R
edger
R
Up reg
genelist
updated 7.7 years ago by
Gordon Smyth
53k • written 7.7 years ago by
drskm7
• 0
0
votes
7
replies
7.4k
views
DESeq estimateSizeFactors() is returning error "Error: all(!is.na(value)) is not TRUE"
deseq2
error
R
estimatesizefactors
zero
updated 3.9 years ago by
LW
• 0 • written 8.4 years ago by
abhishek.yedugondla
• 0
3
votes
2
replies
7.3k
views
Trying to understand differential gene expression through Venn Diagrams from the 'limma' R package: why is there a number outside my diagram?
limma
r
venn diagram
differential expression
updated 11.3 years ago by
James W. MacDonald
68k • written 11.3 years ago by
hmg
• 0
0
votes
1
reply
7.2k
views
Subset data within DeSeq results object
deseq2
R
rna-seq
updated 8.5 years ago by
Michael Love
43k • written 8.5 years ago by
aorvedahl
• 0
0
votes
2
replies
7.1k
views
[Resolved] RcppArmadillo pckg ERRORS : non-zero exit status (and so DESeq2 also)
DESEq2
R
linux
RcppArmadillo
7.0 years ago
RS1
• 0
5
votes
22
replies
7.0k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor
annotationforge
annotationdbi
annotation
r
updated 9.6 years ago by
Axel Klenk
★ 1.1k • written 11.0 years ago by
Stephen H
• 0
8
votes
9
replies
7.0k
views
could not find symbol "keepNA" in environment of the generic function
R
function
genomicalignments
genomicranges
summarizeoverlaps
updated 10.6 years ago by
Mathilde
• 0 • written 10.7 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
5
replies
7.0k
views
SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
R
bioconductor
singlecellexperiment
single cell
updated 8.3 years ago by
lahrmannu
• 0 • written 8.4 years ago by
Walter F. Baumann
▴ 10
0
votes
2
replies
6.9k
views
Converting Fastq to Fasta in R
R
Bioinformatics
Fastq
Fasta
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
christinafragel
• 0
0
votes
2
replies
6.9k
views
Unable to install any bioconductor packages
R
biocinstaller
bioclite
package installation
8.5 years ago
sebastien200109
• 0
3
votes
6
replies
6.8k
views
WGCNA gene significance and module membership
WGCNA
R
updated 3.3 years ago by
Peter Langfelder
★ 3.0k • written 6.3 years ago by
VictoriaL
• 0
1
vote
22
replies
6.8k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor
R
annotationforge
updated 9.1 years ago by
theobroma22
▴ 10 • written 9.6 years ago by
wssdandan2009
• 0
0
votes
1
reply
6.7k
views
Reordering clusters when plotting pheatmap in R
R
pheatmap
clusters
6.7 years ago
ecg1g15
▴ 30
7
votes
3
replies
6.6k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r
limma
voom
vsn
updated 3.3 years ago by
Gordon Smyth
53k • written 7.0 years ago by
Sebastian Hesse
▴ 70
0
votes
2
replies
6.6k
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 3.9 years ago by
kent.riemondy
▴ 20 • written 4.0 years ago by
svenbioinf
• 0
7
votes
9
replies
6.6k
views
WGCNA - networking RNA seq gives only one module!
WGCNA
R
network
co-expression
updated 3.1 years ago by
Peter Langfelder
★ 3.0k • written 6.8 years ago by
avelarbio46
▴ 10
4
votes
3
replies
6.6k
views
Splitting a GRanges object into List of GRange objects by position.
R
granges
subsett
grangeslist
group
updated 9.1 years ago by
Mike Smith
★ 6.6k • written 9.1 years ago by
RichardJActon
▴ 50
3
votes
16
replies
6.5k
views
How to add pseudocount to DESeq2 dds object
deseq2
r
updated 4.3 years ago by
Stanley
▴ 10 • written 5.4 years ago by
Jitendra
▴ 10
2
votes
6
replies
6.5k
views
How can I use geom_label_repel with EnhancedVolcano?
ggrepel
RNASeq
R
EnhancedVolcano
4.6 years ago
Loren
▴ 10
5
votes
1
reply
6.5k
views
RNAseq analysis: what comes first, filtering or normalization
edger
R
rnaseq
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
apfelbapfel
▴ 30
4
votes
6
replies
6.4k
views
WARNING: remove set.seed usage in R code
R
bioccheck
updated 7.7 years ago by
shepherl
4.3k • written 7.7 years ago by
xyluo1991
• 0
5
votes
14
replies
6.4k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape
r
network
graphBAM object
updated 10.2 years ago by
Dan Tenenbaum
★ 8.2k • written 10.2 years ago by
alptaciroglu
▴ 50
2
votes
4
replies
6.3k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
3.2 years ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
6.3k
views
Error in cleanContrast
deseq2
r
error
updated 9.2 years ago by
Michael Love
43k • written 9.2 years ago by
lauren.fitch
• 0
2
votes
3
replies
6.3k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
4.1 years ago
amir.khan
• 0
2
votes
27
replies
6.3k
views
CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for regions < 200kb
crisprseek
sgrna
crispr
cas9
R
10.4 years ago • updated 10.3 years ago
alexgraehl
▴ 20
1
vote
3
replies
6.2k
views
Load FlowCore to read .fcs files in R
flowcore
flow cytometry
R
7.7 years ago
Bayram Sarilmaz
• 0
3
votes
26
replies
6.2k
views
How to prepare targets.txt file in codelink.
r
codelink
updated 10.8 years ago by
Diego Diez
▴ 760 • written 10.9 years ago by
Agaz Hussain Wani
▴ 260
2
votes
4
replies
6.2k
views
edgeR and batch effect correction for differential analysis
edger
limma
r
rnaseq
batcheffect
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
m93
• 0
1
vote
4
replies
6.2k
views
do.call error "second argument must be a list" with GRanges object [closed]
r
error handling
9.1 years ago
Jurat Shahidin
▴ 80
5
votes
4
replies
6.1k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r
ChIPpeakAnno
8.9 years ago • updated 8.6 years ago
salamandra
▴ 20
3
votes
6
replies
6.0k
views
Principle component analysis plot with gene expression data
r
pca
rnaseq
edger
ggbiplot
updated 7.8 years ago by
James W. MacDonald
68k • written 7.8 years ago by
Biologist
▴ 120
3
votes
6
replies
6.0k
views
Affymetrix miRNA 4.0 Normalization and Analysis
R
Limma
microarray
miRNA
updated 4.8 years ago by
S
▴ 10 • written 10.0 years ago by
Radek
▴ 90
3
votes
16
replies
5.9k
views
Any way to proceed duplicate removal for list of GRanges object ?
r
grangeslist
duplicate
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
Jurat Shahidin
▴ 80
10
votes
5
replies
5.9k
views
Normalise to a housekeeping gene in DESEq2
DESeq2
housekeeping
R
RNASeqData
5.3 years ago • updated 5.2 years ago
ecg1g15
▴ 30
0
votes
3
replies
5.8k
views
Rhdf5lib install problems
R
bioconductor
rhdf5
biocmanager
3.5
7.3 years ago
cem45
• 0
5
votes
10
replies
5.8k
views
what should I do with many zero counts from Salmon quantification
Salmon
DESeq2
normalization
r
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
lkianmehr
• 0
0
votes
7
replies
5.7k
views
Can't match on some, but not all, Illumina probe IDs using biomaRt
R
biomart
illumina human ht-12 v4
updated 10.2 years ago by
Thomas Maurel
▴ 800 • written 10.2 years ago by
charkerrhodes
• 0
9
votes
7
replies
5.7k
views
WGCNA: relate modules to binary trait
WGCNA
module
eigengene
binary trait
R
updated 7.1 years ago by
pedrostrusso
▴ 30 • written 7.2 years ago by
Lin
▴ 50
1,163 results • Page
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Comment: Can sample-level weights be used when analysing GSVA scores in limma?
by
A.Barden
▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions
by
Gordon Smyth
53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack
by
a2a2hd42aa
• 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
by
strawberry3
• 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
by
James W. MacDonald
68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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