Showing : RNASeqData • reset
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 7 days ago by ★ 1.2k • written 8 days ago by • 0
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4
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184
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enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
19 days ago • updated 14 days ago ruba-mahmoud • 0
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2
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159
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 26 days ago by • 0
2
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3
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271
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RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 7 weeks ago by • 0 • written 8 weeks ago by • 0
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2
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217
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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 12 weeks ago by ▴ 30 • written 12 weeks ago by • 0
2
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5
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323
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 3 months ago by • 0
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2
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235
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RNA-Seq and disease outcome analysis
rnaseqAnalysis RNASeqData
3 months ago JonasEnder • 0
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3
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265
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 3 months ago by 47k • written 3 months ago by • 0
1
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2
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221
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Installation of R-packages for RNA-seq analysis
RNASeqData
3 months ago Begin-R • 0
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1
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173
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 4 months ago by ★ 2.9k • written 4 months ago by • 0
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183
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Differential RNA seq on TCGA set
DESeq2 RNASeqData
updated 4 months ago by ★ 2.9k • written 4 months ago by • 0
1
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4
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317
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Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
4 months ago Iwan • 0
0
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1
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269
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Using DESeq2 for time-series analysis with two conditions
DESeq2 RNASeqData
updated 5 months ago by ★ 2.9k • written 5 months ago by • 0
0
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1
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322
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 6 months ago by 47k • written 6 months ago by • 0
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230
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how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
8 months ago marymshahi2021 • 0
1
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2
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840
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Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 9 months ago by ★ 1.2k • written 9 months ago by • 0
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215
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Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData RNASeq
10 months ago Pang • 0
0
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1
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348
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I have a query regarding differential gene expression using limma-voom.
RNASeqData DESeq2
updated 10 months ago by 47k • written 10 months ago by • 0
1
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7
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682
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DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 10 months ago by 63k • written 10 months ago by • 0
2
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9
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1.2k
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
11 months ago Peipei • 0
1
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5
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609
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Error in DEseq
DEseq RNASeqData
updated 11 months ago by ★ 2.9k • written 11 months ago by • 0
1
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1
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406
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NOIseq Probability column
RNAseq RNASeqData NOISeq
12 months ago • updated 11 months ago Pratibha ▴ 10
3
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3
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638
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How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
12 months ago JK Kim ▴ 20
0
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2
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856
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How to run vst transformation
RNASeqData vst
updated 12 months ago by 40k • written 13 months ago by • 0
2
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3
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610
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
13 months ago Maka • 0
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5
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1.2k
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
13 months ago • updated 12 months ago priyanka.m • 0
22
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14
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4.8k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 12 months ago by • 0 • written 13 months ago by ▴ 50
0
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2
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726
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Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 13 months ago by 40k • written 13 months ago by ▴ 30
3
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2
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512
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DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
14 months ago • updated 13 months ago Dakarai ▴ 10
0
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1
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424
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 14 months ago by 40k • written 14 months ago by • 0
0
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2
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597
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lncRNA Genes in a Dataset
ncRNAtools RNASeqData
14 months ago sushimoto • 0
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317
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edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
14 months ago Mafalda • 0
1
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4
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696
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
14 months ago sushimoto • 0
0
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0
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385
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How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
14 months ago treebig44 ▴ 30
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467
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high number of reads mapped to too many loci
RNASeqData
14 months ago vasa.broz • 0
0
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1
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344
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
14 months ago karl.stamm ▴ 10
4
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1
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1.3k
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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 14 months ago by 40k • written 14 months ago by ▴ 30
1
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1
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417
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Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 14 months ago by 40k • written 14 months ago by ▴ 30
2
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6
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5.8k
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
14 months ago treebig44 ▴ 30
0
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1
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977
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Limma interaction term
RNASeqData limma DifferentialExpression
updated 14 months ago by 47k • written 14 months ago by • 0
1
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2
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459
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
14 months ago m.glymenaki • 0
1
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1
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444
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edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 15 months ago by 47k • written 15 months ago by • 0
4
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3
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692
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 15 months ago by ★ 1.2k • written 15 months ago by ▴ 10
0
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2
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476
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Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
16 months ago Raito92 ▴ 60
0
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1
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760
views
'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
16 months ago • updated 15 months ago bas_work ▴ 10
1
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1
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554
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Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 19 months ago by 47k • written 19 months ago by • 0
2
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4
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759
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
21 months ago khaveh ▴ 10
0
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2
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574
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Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
22 months ago szomolay • 0
0
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1
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483
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Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 24 months ago by ▴ 710 • written 24 months ago by • 0
0
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3
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616
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Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 24 months ago by ★ 1.2k • written 24 months ago by • 0
50 results • Page 1 of 1
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Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth thank you, yes, please find the targets frame below. Basically, I want to create a design matrix and binarize by 0 and 1 to be…
Comment: WGCNA: many over and under-expressed features in modules of a signed network by andres.firrincieli ▴ 50
answered in Biostars: https://www.biostars.org/p/9564943/
Comment: Multitasking and Rbwa by Jean-Philippe Fortin • 0
Indeed, one can pass additional arguments to the `bwa_aln` function in `Rbwa`: bwa_aln(type="single", index_prefix=index_pr…
Comment: biomaRt error: database disk image is malformed by Emile • 0
UNBORKING the bioMaRt cache `biomaRt::biomartCacheClear()` also fixes the troubles with PANTHER.db installation which have also something t…
Answer: Proteomics data with NA values by Laurent Gatto 1.6k
- First, you need to assess how many missing values you have. - I would recommend not to impute your data by 0 (or any arbitrary small …
Votes
Answer: Question on constructing design matrix and defining contrasts for analysis
WGCNA: many over and under-expressed features in modules of a signed network
Comment: WGCNA: many over and under-expressed features in modules of a signed network
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Answer: Normalized counts from LRT or Wald test?
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