0
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5
replies
4.9k
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Error in (function (classes, fdef, mtable)
software error DECIPHER
updated 5.8 years ago by 4.3k • written 5.8 years ago by • 0
3
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3
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1.5k
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IHW: retain annotation columns in data when running `ihw(pvalue ~ covariate, data = ...)`
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5.8 years ago david.laehnemann ▴ 10
0
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0
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1.4k
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Deconvolution methods from WGBS data (methylation)
methylCC deconvolution methylation dmrseq serum
5.8 years ago marcin.bazyliszek • 0
4
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0
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Tutorial: How to post Salmon data to GEO for use with tximeta
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5.8 years ago Michael Love 43k
0
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0
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ChIPQC cross-coverage plot
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5.8 years ago tuteja.reetu • 0
1
vote
5
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Limma for proteomic data! Please Help!
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updated 5.8 years ago by 53k • written 5.8 years ago by • 0
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3.8k
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Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 60
5
votes
11
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Heatmap only including DE genes?
heatmap coolmap pheatmap
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 60
3
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5
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2.4k
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Different numbers of DE genes using edgeR and DESEQ2
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updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 60
6
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6
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3.3k
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GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 60
1
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2
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2.1k
views
Is this an issue? "Error in (function (x) : attempt to apply non-function" when calling tximeta::summarizeToGene(se) for the first time with some da…
software error tximeta
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
0
votes
21
replies
4.7k
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How to use DECIPHER to design group-specific primers
Decipher
5.8 years ago hoonhuiyi • 0
0
votes
10
replies
1.6k
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Java & DESeq2
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 20
1
vote
11
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3.4k
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Error uploading deseq2
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updated 5.8 years ago by 25k • written 5.8 years ago by • 0
1
vote
2
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869
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trans-effect analysis with DESeq2
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
votes
1
reply
1.6k
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 5.8 years ago by ★ 29k • written 6.4 years ago by ▴ 20
3
votes
3
replies
2.2k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 5.8 years ago by ★ 29k • written 5.8 years ago by ▴ 10
0
votes
2
replies
3.6k
views
How to use DESeqDataSetFromHTSeqCount
deseq2
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by ▴ 20
3
votes
3
replies
2.6k
views
Can't install graph package
graph
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 10
2
votes
16
replies
2.7k
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DESeq2 annotation file
annotation
5.8 years ago zen • 0
0
votes
11
replies
3.2k
views
DESeq2 generating different DEGs based on the order of samples listed in the colData = samples file
DESeq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
votes
1
reply
684
views
Reverse calculate counts using DESeq2 normalised values
deseq2 rnaseq
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
0
replies
1.2k
views
Is rnb.execute.import() has a bug in reading bismarkCytosine formart bed file? coordinates seem to be shifted by 1
RnBeads
5.8 years ago caoy4g4 • 0
2
votes
5
replies
7.6k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 5.8 years ago by ▴ 10
2
votes
2
replies
3.3k
views
how to do normalization using edgeR
edger
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 40
0
votes
2
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1.3k
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Parsing error creating tx2gene object for tximport
tximport GCF feature table parsing error chromosome
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
874
views
DESeq2 - why genes with very large variance between reps show up as significantly changed?
deseq2
5.8 years ago ninova • 0
2
votes
4
replies
1.5k
views
Error in "Relating the consensus modules to female set-specific modules"
WGCNA
updated 3.6 years ago by ▴ 10 • written 5.8 years ago by ▴ 60
0
votes
1
reply
811
views
biomaRt: The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
biomart
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
0
votes
1
reply
1.4k
views
Gene Co-Expression Network using Pearsons Correlation
coexnet
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
0
votes
0
replies
983
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Polyester - simulate_experiment_countmat with gtf
polyester
5.8 years ago liorglic ▴ 10
1
vote
2
replies
2.5k
views
Rsubread buildindex error
Rsubread
updated 5.8 years ago by ★ 3.6k • written 5.8 years ago by ▴ 10
0
votes
1
reply
2.9k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
votes
3
replies
966
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DESeq2 library problem
R deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
votes
2
replies
1.2k
views
edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 20
0
votes
3
replies
2.1k
views
ERROR: dependency 'AnnotationDbi' is not available for package 'hgu133plus2cdf'
normalization
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
0
votes
2
replies
1.3k
views
Slingshot - residual_variance
Slingshot
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 330
0
votes
0
replies
810
views
ChromPlot not takin a regular data.frame as input
ChromPlot
5.8 years ago daniel.gautheret • 0
0
votes
1
reply
1.6k
views
Multi-level experiment with continuous varibles and confounders in limma
limma de differential gene expression multi-tissue design multi-level design
updated 5.8 years ago by ★ 29k • written 5.8 years ago by • 0
0
votes
1
reply
1.1k
views
Comparison of cydar to other Bioconductor packages for flow cytometry analysis
cydar
updated 5.8 years ago by ★ 29k • written 5.8 years ago by ▴ 10
0
votes
2
replies
713
views
Changes in expression associated with changes in cell count using limma
limma model selection several covariables pre-post whole blood
5.8 years ago p.figuerola.9 • 0
0
votes
1
reply
843
views
How to upload a custom genome build at Galaxy
annotation
5.8 years ago vidar.blikstad • 0
0
votes
3
replies
1.6k
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Normalization of RNA seq data
RNA seq cpm
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
0
votes
1
reply
2.8k
views
Using DeSeq2 on microRNA data
deseq2 mirdeep2 microRNA differential expression analysis
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
1.2k
views
Custom pathway for limma's kegga?
limma
5.8 years ago Ahdee ▴ 60
4
votes
3
replies
1.7k
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 10
1
vote
3
replies
1.1k
views
DESeq2 / agricolae packages conflict
deseq2 dependendies conflict agricolae
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
votes
2
replies
552
views
rlog transformation for downstream analyses in DESeq2: Importance of experiment design
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
3
replies
2.0k
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Topgo, Deseq and KEGG pathway
annotation cancer
updated 5.8 years ago by 4.3k • written 5.8 years ago by • 0
0
votes
0
replies
350
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EBSeqHMM EBSeqHMMTest function error
software error
5.8 years ago xinyunie • 0
46,730 results • Page 171 of 935
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Comment: Are individual-mouse-based statistics possible in CellChat? by LillianaVolkman99 • 0
thank you very much. https://www.biostars.org/p/9617271/
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …
Answer: Bile acid analysis with limpa by Gordon Smyth 53k
I am not familiar with targeted HPLC-MS and I don't know what you mean by "peak areas". If it produces standard format mass spec data from …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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