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
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Archives prior to 3.15 gone
archive bioconductor
updated 6 months ago by 3.9k • written 20 months ago by ▴ 30
0
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17
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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
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5
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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
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3
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2.1k
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maSigPro genes from clusters
masigpro clustering
updated 17 hours ago by • 0 • written 7.9 years ago by • 0
2
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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
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3
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2.2k
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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
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2.6k
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problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.2 years ago by • 0
0
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2
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241
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
7 weeks ago • updated 6 weeks ago w.cookson • 0
4
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9
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1.4k
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RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
1
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3
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439
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
6
votes
19
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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
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7
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1.8k
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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
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9
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1.4k
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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
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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
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Heat Map
ColData pheatmap DESeq2
written 11 months ago by • 0
15
votes
17
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1.3k
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Why p value inconsistent when using different number of pathway score?
limma
27 days ago • updated 16 days ago Chris ▴ 10
4
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4
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3.5k
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Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 3.2 years ago by ▴ 20
0
votes
2
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878
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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
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5
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6.3k
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Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 8 months ago by 50k • written 2.5 years ago by ▴ 340
0
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3
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4.4k
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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
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
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6
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1.5k
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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
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2
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710
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DESeq2 batch design
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
4
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7
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898
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weird volcano plot
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updated 10 weeks ago by • 0 • written 6 months ago by ▴ 10
0
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5
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DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.2 years ago • updated 12 days ago Henrik Bengtsson ★ 2.4k
0
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2
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305
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
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3
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3
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368
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permutation test in edgeR
rna-seq edgeR
updated 27 days ago by 50k • written 5 weeks ago by • 0
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Differential expression analysis: Permutation Test
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updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
2
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2
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locfunc not found in DESeq2
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12 weeks ago Hope ▴ 10
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6
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Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 7 months ago by 700 • written 21 months ago by ▴ 20
0
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2
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160
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DESeq2 v1.35.0
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
3
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3
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414
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plotUMAP Gene Set Faceted
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updated 3 months ago by ▴ 160 • written 3 months ago by ★ 1.5k
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3
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Filtering low intensity probes in microarray data
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3
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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
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21
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deseq2 filter the low counts
deseq2 lowcount
updated 4 months ago by • 0 • written 9.2 years ago by ▴ 40
0
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3
replies
373
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Sign Output Values PADOG
PADOG
updated 6 months ago by • 0 • written 6 months ago by • 0
1
vote
6
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760
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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
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1.1k
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Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago Ndimensional ▴ 20
9
votes
38
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6.8k
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manipulate bedpe format files
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written 8.3 years ago by ▴ 190
0
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4
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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
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3
replies
1.9k
views
Making MDS plot
plotMDS limma
updated 11 months ago by 50k • written 11 months ago by • 0
1
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8
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2.8k
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Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
0
votes
2
replies
349
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Running DESeq on normalized data
deseq DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
0
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6
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919
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
1
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7
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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
0
votes
5
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9.3k
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tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 8 weeks ago by • 0 • written 7.6 years ago by • 0
6
votes
7
replies
968
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 7 months ago by ▴ 20
4
votes
2
replies
1.3k
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Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 10 months ago by 50k • written 10 months ago by ▴ 10
1,737 results • Page 2 of 35
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
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" …
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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