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Votes
3
votes
2
replies
1.3k
views
error when I use groHMM on data outside of the tutorial
grohmm
groseq
next-generation sequencing
R
5.7 years ago
Deleted
▴ 70
3
votes
4
replies
2.4k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks
tcga
genomicdatacommon
5.8 years ago
franceschini.gianmarco
• 0
2
votes
4
replies
2.2k
views
Error downloading Homo.sapiens package
Homosapiens
updated 3.6 years ago by
James W. MacDonald
66k • written 3.6 years ago by
noemicarrascoyepes
▴ 20
2
votes
5
replies
3.9k
views
Warning in R
software error
9.0 years ago
Angel
▴ 40
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge
GSEA
clusterprofiler
GO
annotation
6.8 years ago
cabezasdelafuented
▴ 10
2
votes
4
replies
1.0k
views
Arrayquality metrics Warning - Warning message in maximumLevels(fac, n = length(colors)):
Wolfgang Huber
microarray
5.3 years ago
RV
▴ 10
2
votes
4
replies
1.8k
views
Problem installing Repitools package
package installation
r package problem
updated 7.6 years ago by
Martin Morgan
25k • written 7.6 years ago by
sumudu_rangika
▴ 20
2
votes
3
replies
1.6k
views
BioConductor Package submission
submit package
tracker
build report
8.1 years ago
thomas.nigel.lawson
• 0
2
votes
2
replies
2.4k
views
Gviz: plotting multiple custom tracks or adding panel legend at the top
gviz
updated 7.5 years ago by
sergisayolspuig
▴ 80 • written 7.6 years ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
1
reply
666
views
"condition" factor name is hardcoded
DEXSeq
7.5 years ago
bjoern.gruening
• 0
2
votes
0
replies
2.0k
views
Complex Limma design: technical replication, biological replication and repeated experiment
Microarray
limma
Microarray
limma
10.8 years ago
Gordon Smyth
50k
2
votes
0
replies
1.6k
views
R: miRNA and validated/predicted target genes
miRNA
miRNA
15.0 years ago
mauede@alice.it
▴ 870
2
votes
0
replies
544
views
NA issue
Normalization
Normalization
19.6 years ago
Antonio
▴ 40
2
votes
4
replies
1.7k
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r
summarizedexperiment
grangeslist
7.2 years ago
Jurat Shahidin
▴ 80
2
votes
2
replies
1.8k
views
Error: could not find function "godata"
gosemsim
5.9 years ago
anton.kratz
▴ 60
2
votes
0
replies
1.9k
views
NanoString Data Normalization Revisited
nanostring
normalization
8.7 years ago
alakatos
▴ 130
2
votes
4
replies
1.1k
views
Mathematical operations in FCS file
flowCore
flow cytometry
4.5 years ago
chandra.swarnendu
• 0
2
votes
2
replies
1.0k
views
aes label in ggbio_1.26.1 with ggplot2_3.0.0
ggbio
ggplot2
5.7 years ago
Lescai, Francesco
▴ 380
2
votes
0
replies
1.1k
views
Discrepancies between sradb, sraruninfo
sradb
6.0 years ago
langmea
▴ 20
2
votes
0
replies
2.0k
views
'Error in summary(lm1)$coefficients[2, 1] : subscript out of bounds' while running pickSoftThreshold in WGCNA
wgcna
picksoftthreshold
6.2 years ago
aditi
▴ 20
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib
rhdf5
3.3 years ago • updated 9 months ago
Thomas Sandmann
▴ 90
2
votes
2
replies
2.9k
views
bioMaRt error : "BioMart webservice returned an invalid result: biomaRt expected a character string of length 1"
r package problem
6.0 years ago
rdpinho
• 0
2
votes
4
replies
1.5k
views
GEOquery: Missing featureNames after creating expression set from series matrix file
geoquery
updated 9.0 years ago by
James W. MacDonald
66k • written 9.0 years ago by
knaxerova
▴ 10
2
votes
3
replies
4.6k
views
No gene set have size > 10 ...
clusterprofiler
gene ontology
5.6 years ago
anton.kratz
▴ 60
2
votes
2
replies
713
views
log transform or not the dependent variable/ covariates
limma
edgeR
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
anna.cot.anna.cot
▴ 30
2
votes
4
replies
1.6k
views
Can't create STRINGdb v11 object using STRINGdb packages methods
stringdb
5.0 years ago
Moosa
• 0
2
votes
0
replies
1.2k
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress
ArrayExpress
11.2 years ago
Ibrahim Emam
▴ 50
2
votes
3
replies
974
views
Differential gene expression using Ballgown
r
normalization
3.8 years ago
lakshmi9c
• 0
2
votes
6
replies
1.2k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
4 months ago • updated 3 months ago
Tobias
• 0
2
votes
1
reply
884
views
DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
diffbind
5.0 years ago
melnuesch
▴ 10
2
votes
5
replies
2.3k
views
convert GAlignmentPairs to GAlignment
GAlignmentPairs
galp2gal
RIPSeeker
9.2 years ago
tomas.bjorklund
▴ 20
2
votes
6
replies
1.3k
views
memory leak when subsampling BAM
GenomicFiles
ShortRead
Rsamtools
3.3 years ago
robmaz77
▴ 20
2
votes
3
replies
8.5k
views
Warning in "countReads" [Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common.]
GreyListChIP
6.6 years ago
kyliecode
• 0
2
votes
0
replies
522
views
Quality Metrics for Graph Clustering for Biological Networks
R
protein-interaction networks
network
4.0 years ago
hamza_karakurt
▴ 60
2
votes
1
reply
842
views
Problem while installing genomicfeatures package.
genomicfeatures
8.3 years ago
vinod.acear
▴ 50
2
votes
0
replies
808
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges
GenomicFeatures
grange
distanceToNearest
R
4.6 years ago
rmash
▴ 20
2
votes
0
replies
1.3k
views
Limma - decideTests - separate/nestedF questions
Microarray
limma
17.2 years ago • updated 5.1 years ago
Gordon Smyth
50k
2
votes
0
replies
956
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
3.3 years ago
Ben
▴ 50
2
votes
3
replies
1.1k
views
Problem in reading .bam files (aligned to transcriptome) with ribofileCR function
R
riboseqr
ribosome profiling
6.3 years ago
bsad
• 0
2
votes
1
reply
655
views
When to Correct for Cell Type Heterogeneity in ChAMP Pipeline
microarray
updated 3.4 years ago by
Ankit
▴ 20 • written 5.3 years ago by
Gurkenkönig
▴ 10
2
votes
15
replies
754
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 3 months ago by
Michael Love
42k • written 3 months ago by
cinzia.spagnoli
• 0
2
votes
1
reply
718
views
Parsing geoms to enrichplot
enrichplot
3.8 years ago
Francois Marchildon
▴ 20
2
votes
0
replies
1.9k
views
Gviz plot combined with multiple ggplot2 plots
gviz
gviz-package
ggplot2
6.8 years ago
christian.aichmueller
▴ 20
2
votes
2
replies
1.1k
views
Using clusterProfiler for depletion analysis
clusterProfiler
enrichGO
2.5 years ago
samsiljee
• 0
2
votes
1
reply
922
views
design matrix for dge
limma
updated 8.0 years ago by
Gordon Smyth
50k • written 8.0 years ago by
1234anjalianjali1234
▴ 30
2
votes
2
replies
1.1k
views
list fo genes by cnv
cnv
genes
genomic ranges
splitByOverlap
updated 7.1 years ago by
Martin Morgan
25k • written 7.1 years ago by
julrodr80
▴ 30
2
votes
4
replies
1.5k
views
rma summarization error when normalizing using oligo and brainarray cdf
oligo
brainarray
mbni
4.9 years ago
Moosa
• 0
2
votes
2
replies
3.0k
views
DiffBind installation fails: Error: package ‘BiocGenerics’ 0.34.0 is loaded, but >= 0.36.0 is required by ‘IRanges’
systemPipeR
Bioconductor
DiffBind
BiocGenerics
updated 3.3 years ago by
Martin Morgan
25k • written 3.3 years ago by
tina
• 0
2
votes
4
replies
1.3k
views
Weird error in Rstudio trying to retreive and load genomic data from external databases
R
software error
Bioconductor
4.3 years ago
svlachavas
▴ 830
2
votes
1
reply
537
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 12 months ago by
andres.firrincieli
▴ 50 • written 12 months ago by
hesse.sebastian
▴ 10
1,000 results • Page
3 of 20
Recent ...
Replies
Comment: Cannot install oligo on Fedora
by
Guido Hooiveld
★ 4.0k
Thanks for all suggestions and getting to the bottom of this! Unfortunately, fixing C code goes way above my skill level, so I cannot contr…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
I think the solution is for the C code in `oligo` to be updated to work with more modern versions of `zlib`. The `zlibbioc` package is real…
Comment: Error in gseDO function
by
Guido Hooiveld
★ 4.0k
I don't fully understand what you are asking... Yet, in my opinion it doesn't make sense to use the results of only 12 genes for ORA (nor G…
Comment: Counter-directional LFC shrinkage
by
ATpoint
★ 4.2k
Is this RNA-seq? The unshrunken MA-plot looks very odd and indicates that normalization is completely offset.
Answer: ChAMP not available for bioconductor 3.19
by
shepherl
3.9k
See https://support.bioconductor.org/p/9158324/#9158336 . We have reached out to goseq to fix the package; we have a community member …
Votes
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
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