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Views
Votes
2
votes
3
replies
253
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Reza
• 0
2
votes
4
replies
279
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 25 days ago by
James W. MacDonald
65k • written 29 days ago by
Mirella Aurora
• 0
2
votes
1
reply
162
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
e1271094
• 0
2
votes
7
replies
360
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
9 days ago • updated 6 days ago
sajadahmad41454
• 0
2
votes
3
replies
262
views
package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by
Gordon Smyth
50k • written 14 days ago by
Patrycja
▴ 20
2
votes
5
replies
304
views
get BM error
ensembldb
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Fara
• 0
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 days ago by
Michael Love
42k • written 11 days ago by
mat149
▴ 70
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 9 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
1
vote
2
replies
255
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
9 days ago • updated 8 days ago
Dylan.Sheerin
• 0
1
vote
0
replies
51
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
3 days ago
Aleena
▴ 30
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
252
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 21 days ago by
Michael Love
42k • written 22 days ago by
JalapenoCornbread
• 0
1
vote
7
replies
357
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
22 days ago • updated 21 days ago
pl23
• 0
1
vote
1
reply
185
views
Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by
Michael Love
42k • written 14 days ago by
Zainab
▴ 10
1
vote
2
replies
82
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
2 days ago
Patadù
▴ 10
1
vote
1
reply
152
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 21 days ago by
Leo Lahti
▴ 40 • written 21 days ago by
Dario Strbenac
★ 1.5k
1
vote
0
replies
346
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
28 days ago
BioinfGuru
▴ 30
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
fernanda.backsouza
▴ 10
1
vote
2
replies
262
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 28 days ago
Weiqian
▴ 10
1
vote
5
replies
514
views
Can't post a question containing code?
Bioconductor
updated 7 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
1
vote
1
reply
155
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
marcusn
• 0
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 25 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
175
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
23 days ago • updated 22 days ago
ATpoint
★ 4.1k
1
vote
3
replies
303
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 days ago by
ATpoint
★ 4.1k • written 16 days ago by
angelathuynh5
• 0
1
vote
2
replies
211
views
Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 11 days ago
Lluís Revilla Sancho
▴ 730
1
vote
2
replies
288
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
17 days ago • updated 16 days ago
Yveto
• 0
1
vote
2
replies
224
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
4 days ago • updated 1 day ago
BioinfGuru
▴ 30
1
vote
4
replies
229
views
minfi::read.metharray.exp
minfiData
minfi
updated 23 days ago by
Basti
▴ 780 • written 25 days ago by
clacarion
• 0
1
vote
3
replies
227
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
Ashley
• 0
1
vote
2
replies
369
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 14 days ago
Kim
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 10 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
1
vote
4
replies
355
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
23 days ago • updated 21 days ago
winwater0928
• 0
1
vote
2
replies
397
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
Kim
• 0
1
vote
4
replies
526
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 16 days ago
JKim
• 0
1
vote
0
replies
319
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
8 weeks ago • updated 3 days ago
shepherl
3.9k
1
vote
2
replies
738
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago
Patadù
▴ 10
1
vote
3
replies
890
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 23 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
235
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
29 days ago
Le
• 0
1
vote
2
replies
178
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago • updated 29 days ago
Sherin
• 0
1
vote
2
replies
116
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
3 days ago • updated 2 days ago
Daniel
• 0
1
vote
2
replies
203
views
Citation for edgeR user guide
edgeR
written 24 days ago by
k___
▴ 30
0
votes
1
reply
82
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 3 days ago by
Michael Love
42k • written 4 days ago by
piemmea
• 0
0
votes
1
reply
39
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
11 hours ago • updated 10 hours ago
shaunpeterson
• 0
0
votes
2
replies
748
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 2 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
1
reply
165
views
Adding columns to DEXSeqResults object
DEXSeq
updated 29 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
1
reply
165
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 12 days ago
Henrik Bengtsson
★ 2.4k
0
votes
4
replies
117
views
error running enricher from clusterprofiler
clusterProfiler
cluster
2 days ago
Yael
• 0
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 13 hours ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
191 results • Page
2 of 4
Recent ...
Replies
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?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
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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