Showing : rnaseqdata • reset
1
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.0 years ago dantasezequiel1 • 0
2
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3
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1.3k
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RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 12 months ago by • 0 • written 12 months ago by • 0
0
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2
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631
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Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 13 months ago by ▴ 30 • written 13 months ago by • 0
1
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7
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791
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
1
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2
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1.1k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
1
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2
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2.5k
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Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 19 months ago by ★ 1.3k • written 19 months ago by • 0
3
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6
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1.3k
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Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
0
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10
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2.8k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 9.8 years ago by ▴ 320 • written 9.8 years ago by ★ 6.8k
0
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1
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317
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by 41k • written 5 months ago by ▴ 10
0
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1
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622
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
0
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1
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1.0k
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RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 8.0 years ago by 41k • written 8.0 years ago by ▴ 80
0
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5
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2.1k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
2.0 years ago • updated 23 months ago priyanka.m • 0
6
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4
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10k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.3 years ago by • 0 • written 3.1 years ago by ▴ 10
3
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4
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1.3k
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.0 years ago hgalmoore • 0
2
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5
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1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 13 months ago by • 0
4
votes
1
reply
2.3k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 30
0
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1
reply
544
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by ▴ 20
0
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3
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724
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 13 months ago by 50k • written 13 months ago by • 0
0
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2
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1.3k
views
How to run vst transformation
RNASeqData vst
updated 23 months ago by 41k • written 23 months ago by • 0
2
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4
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2.8k
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Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
3.4 years ago ecg1g15 ▴ 20
0
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6
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748
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 8 months ago by 50k • written 8 months ago by • 0
0
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2
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614
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RNA-Seq and disease outcome analysis
rnaseqAnalysis RNASeqData
13 months ago JonasEnder • 0
3
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2
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915
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
3.1 years ago Wuschel ▴ 10
22
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15
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7.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
1
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1
reply
632
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 30
4
votes
3
replies
1.2k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 2.2 years ago by ★ 1.3k • written 2.2 years ago by ▴ 10
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2
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316
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
0
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1
reply
549
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
1
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1
reply
568
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
1
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1
reply
390
views
Deseq contrast question
RNASeqData DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 10
1
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2
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1.5k
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Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 9.2 years ago by ★ 2.0k • written 9.2 years ago by ▴ 150
0
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2
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760
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Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
2.2 years ago Raito92 ▴ 60
2
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8
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2.3k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.0 years ago by 50k • written 3.0 years ago by ▴ 20
0
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2
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1.1k
views
lncRNA Genes in a Dataset
ncRNAtools RNASeqData
2.0 years ago sushimoto • 0
1
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2
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500
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I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 8 months ago by 41k • written 9 months ago by • 0
1
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4
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1.0k
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
2.1 years ago • updated 2.0 years ago sushimoto • 0
0
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4
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628
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 6 months ago by 65k • written 6 months ago by ▴ 10
0
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6
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1.2k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
3.0 years ago Rishav ▴ 20
2
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9
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2.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
22 months ago Peipei • 0
1
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4
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1.2k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
15 months ago Iwan • 0
3
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3
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1.3k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
22 months ago JK Kim ▴ 20
0
votes
1
reply
620
views
HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
2.1 years ago karl.stamm ▴ 10
1
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6
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1.3k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.2 years ago Seaweed • 0
1
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1
reply
1.1k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 2.5 years ago by 50k • written 2.5 years ago by • 0
1
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1
reply
307
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
1
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2
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648
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Installation of R-packages for RNA-seq analysis
RNASeqData
14 months ago Begin-R • 0
0
votes
3
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655
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
4 months ago Oenone • 0
8
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2
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6.7k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
2
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4
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1.2k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
2.6 years ago khaveh ▴ 10
7
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5
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3.3k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.4 years ago ecg1g15 ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by jacques.imbert • 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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