Showing : r • reset
23
votes
6
replies
26k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 4 months ago by ▴ 20 • written 5.6 years ago by ▴ 50
22
votes
14
replies
2.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 3 months ago by • 0 • written 4 months ago by ▴ 50
14
votes
14
replies
23k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 7 weeks ago by • 0 • written 5.1 years ago by ▴ 20
6
votes
11
replies
5.5k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 8 months ago by ▴ 40 • written 6.5 years ago by ▴ 70
5
votes
14
replies
2.9k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3 months ago by ★ 1.4k • written 4.1 years ago by ▴ 50
5
votes
3
replies
931
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
3 months ago kieran.short ▴ 30
4
votes
4
replies
201
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
18 days ago • updated 14 days ago L • 0
4
votes
3
replies
2.2k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 7 months ago by • 0 • written 5.1 years ago by • 0
4
votes
8
replies
593
views
R package installation error
HPC R Bioconducter
4 months ago nabiyogesh ▴ 10
4
votes
6
replies
328
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
3 months ago • updated 12 weeks ago mohammedtoufiq91 ▴ 10
4
votes
2
replies
151
views
good-first-issue (or similar) GitHub
Culture R GitHub
updated 27 days ago by 37k • written 27 days ago by • 0
4
votes
6
replies
609
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
10 months ago s-rhussien • 0
4
votes
4
replies
289
views
motifStack Plotting the correct data positions on x axis
motifStack R
5 months ago Marwah • 0
3
votes
4
replies
606
views
DiffBind (Error in if (DBA$config$parallelPackage))
parallel R DiffBind
updated 8 months ago by ★ 4.4k • written 11 months ago by • 0
3
votes
3
replies
227
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 12 weeks ago by 46k • written 12 weeks ago by ▴ 10
3
votes
3
replies
332
views
Limma vs deseq2 results
limma RNASeq R
11 weeks ago • updated 10 weeks ago k___ ▴ 20
3
votes
4
replies
648
views
STRINGdb: Error in download.file(urlStr, temp)
STRINGdb R
updated 7 months ago by ▴ 70 • written 9 months ago by ▴ 10
3
votes
2
replies
218
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
4 months ago • updated 3 months ago Dakarai ▴ 10
3
votes
16
replies
1.9k
views
How to add pseudocount to DESeq2 dds object
deseq2 r
updated 9 months ago by ▴ 10 • written 23 months ago by ▴ 10
2
votes
5
replies
633
views
DESeq2: error while ploting figure
R DESeq2
updated 9 months ago by 37k • written 9 months ago by • 0
2
votes
3
replies
260
views
Confused about the design matrix in edgeR: How to tell R to consider one level as a reference and the other is a treatment to be compared to that ref.
R edgeR
updated 11 weeks ago by 46k • written 11 weeks ago by • 0
2
votes
2
replies
330
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
6 months ago Hasan Alanya • 0
2
votes
9
replies
348
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
8 weeks ago • updated 7 weeks ago Peipei • 0
2
votes
1
reply
155
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 3 months ago by ▴ 70 • written 3 months ago by • 0
2
votes
2
replies
1.9k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 10
2
votes
3
replies
587
views
fgsea not downloading due to new r version. Is there a way around this?
r fgsea
6 months ago amir.khan • 0
2
votes
2
replies
761
views
Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
11 months ago jbnrodriguez ▴ 10
2
votes
3
replies
340
views
Ensembl non responsive
ensembl R
4 months ago ksci ▴ 10
1
vote
9
replies
1.5k
views
Handling DNA sequence loaded from a file
r biostrings DNAsequence
updated 8 weeks ago by 60k • written 6.4 years ago by ▴ 260
1
vote
1
reply
176
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by • 0
1
vote
3
replies
397
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 7 months ago by 37k • written 7 months ago by • 0
1
vote
3
replies
250
views
GVIZ giving error with loading hg38 genome
R Gviz
3 months ago RUser743 • 0
1
vote
4
replies
608
views
Remove box frame from vennDiagram plot in limma
Limma venndiagram r
updated 8 months ago by • 0 • written 4.0 years ago by • 0
1
vote
1
reply
222
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 12 weeks ago by 46k • written 3 months ago by • 0
1
vote
3
replies
229
views
Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 5 months ago by ▴ 390 • written 5 months ago by • 0
1
vote
10
replies
844
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
9 months ago • updated 8 months ago Ming ▴ 360
1
vote
5
replies
356
views
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
clusterProfiler r
updated 3 months ago by ★ 3.3k • written 3 months ago by • 0
1
vote
2
replies
242
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
12 weeks ago • updated 11 weeks ago takemoto • 0
1
vote
1
reply
97
views
roughDispEstimate and momentsDispEstimate
estimator roughmethodofmoments DESeq2 R Code
updated 8 weeks ago by ▴ 390 • written 8 weeks ago by • 0
1
vote
0
replies
89
views
Mapping patient dataset onto control dataset
Cytometry R Data
6 weeks ago hamiltond ▴ 10
0
votes
2
replies
152
views
R Bioconductor package Affxparser keeps crashing
affxparser r Bioconductor
updated 9 weeks ago by 60k • written 9 weeks ago by • 0
0
votes
0
replies
278
views
Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
8 months ago Paulina • 0
0
votes
6
replies
270
views
regression analysis for epic array methylation data using limma
limma Epigenetics STATISTICS R
12 weeks ago nabiyogesh ▴ 10
0
votes
0
replies
167
views
Job: Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology
clinical R bioinformatics multiomics oncology
4 months ago vincent.piras • 0
0
votes
1
reply
429
views
How can i download maf files form GDC Data Portal?
maf R
updated 4 months ago by 3.6k • written 4 months ago by • 0
0
votes
1
reply
155
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 3 months ago by 37k • written 3 months ago by • 0
0
votes
1
reply
464
views
values (NA) in p value Deseq2 (reopen)
pvalue NA R DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
0
votes
1
reply
212
views
trouble installing DESeq2
install packages R DESeq2
updated 3 months ago by 3.2k • written 3 months ago by • 0
0
votes
1
reply
95
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 13 days ago by 46k • written 14 days ago by • 0
0
votes
6
replies
380
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
6 weeks ago Mohamed • 0
50 results • Page 1 of 1
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Answer: mapToAlignments_issue by Hervé Pagès 15k
> I would expect in case of reverse alignment lifted ranges to correspond to position 91-100 of the query sequence. Nope. Local coordinate…
Answer: Problem related to `biomaRt::getBM()` during `R CMD check` execution by James W. MacDonald 60k
Does the section in the biomaRt vignette that talks about caching (and using a temp dir) help?
Comment: OPLS-DA: confidence interval for accuracy metric by Eddie • 0
Worked well under pROC. Thank you
Comment: errors in annotation by James W. MacDonald 60k
If you go to NCBI and the data appear to be correct, then they have evidently already fixed the errors you have found. The data we download…
Comment: How should I set my eps value in cluster profiler? by Guido Hooiveld ★ 3.3k
Under the hood `clusterProfiler` makes use of a (fast) GSEA algorithm implemented in the package `fgsea` (function `fgseaMultilevel`). The …
Votes
A: EGSEA error during report generation: "only 0's may be mixed with negative subsc
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
How to select summit size for histone ChiP-Seq in Diffbind
Comment: GSEA with Wikipathways not entirely reproducible
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