14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by • 0 • written 8.4 years ago by ▴ 60
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive bioconductor
updated 6 months ago by 3.9k • written 20 months ago by ▴ 30
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 11 months ago by • 0 • written 6.6 years ago by • 0
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.3 years ago by ▴ 10
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro clustering
updated 7 hours ago by • 0 • written 7.9 years ago by • 0
2
votes
2
replies
406
views
"Details" section for specific software packages
Website
updated 7 months ago by ★ 6.5k • written 7 months ago by • 0
2
votes
3
replies
2.2k
views
Keep getting this error "Warning: unable to access index for repository"?
CATALYST
updated 12 months ago by 16k • written 12 months ago by ▴ 20
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.2 years ago by • 0
0
votes
2
replies
241
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
7 weeks ago • updated 6 weeks ago w.cookson • 0
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
1
vote
3
replies
438
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 17 days ago by • 0 • written 4.6 years ago by ▴ 10
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 19 months ago by ▴ 20
0
votes
4
replies
649
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
9 months ago anne.hoffrichter • 0
4
votes
9
replies
1.4k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 9 months ago by ▴ 10 • written 9 months ago by ▴ 10
2
votes
5
replies
1.4k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
2
replies
566
views
Heat Map
ColData pheatmap DESeq2
written 11 months ago by • 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
27 days ago • updated 16 days ago Chris ▴ 10
4
votes
4
replies
3.5k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 3.2 years ago by ▴ 20
0
votes
2
replies
878
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by 42k • written 9 months ago by • 0
6
votes
5
replies
6.3k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 8 months ago by 50k • written 2.5 years ago by ▴ 340
0
votes
3
replies
4.3k
views
The MicrobiotaProcess package performed lefse analysis and had a problem drawing the tree
MicrobiotaProcess offspring.tbl_tree_item
updated 9 months ago by • 0 • written 9 months ago by • 0
1
vote
3
replies
504
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by • 0 • written 4 months ago by • 0
0
votes
2
replies
498
views
plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
2
votes
6
replies
1.5k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 6 weeks ago by ▴ 180 • written 5 months ago by ▴ 10
1
vote
2
replies
709
views
DESeq2 batch design
DESeq2
updated 8 months ago by ★ 1.4k • written 9 months ago by ▴ 10
4
votes
7
replies
898
views
weird volcano plot
DESeq2
updated 10 weeks ago by • 0 • written 6 months ago by ▴ 10
1
vote
2
replies
685
views
unable to retrieve certain packages from bioconductor 3.15
Bioconductor biocondu
updated 9 months ago by 65k • written 9 months ago by ▴ 10
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
2
replies
305
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 25 days ago shepherl 3.9k
2
votes
2
replies
329
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
12 weeks ago Hope ▴ 10
7
votes
6
replies
4.2k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 7 months ago by 700 • written 21 months ago by ▴ 20
0
votes
2
replies
159
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
3
votes
3
replies
413
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by ▴ 160 • written 3 months ago by ★ 1.5k
2
votes
3
replies
3.1k
views
Filtering low intensity probes in microarray data
Hugene1.0 ST
written 6.8 years ago by ▴ 50
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 17 days ago by • 0 • written 13.1 years ago by ▴ 10
28
votes
21
replies
49k
views
deseq2 filter the low counts
deseq2 lowcount
updated 4 months ago by • 0 • written 9.2 years ago by ▴ 40
0
votes
3
replies
373
views
Sign Output Values PADOG
PADOG
updated 6 months ago by • 0 • written 6 months ago by • 0
1
vote
6
replies
760
views
Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 11 weeks ago by 65k • written 3 months ago by • 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago Ndimensional ▴ 20
9
votes
38
replies
6.8k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.3 years ago by ▴ 190
0
votes
4
replies
3.7k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat singleR
updated 10 months ago by • 0 • written 4.5 years ago by • 0
1
vote
3
replies
1.9k
views
Making MDS plot
plotMDS limma
updated 11 months ago by 50k • written 11 months ago by • 0
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
0
votes
2
replies
349
views
Running DESeq on normalized data
deseq DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
0
votes
6
replies
919
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
1
vote
7
replies
6.8k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 11 weeks ago by 16k • written 6 months ago by ▴ 10
1,000 results • Page 2 of 20
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
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
WEHI, Melbourne, Australia, just now
United States, 13 minutes ago
United States, 17 minutes ago
San Diego, 26 minutes ago
Sweden, 40 minutes ago
Traffic: 795 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6