Showing : rnaseqdata • reset
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 6 days ago by • 0 • written 17 months ago by • 0
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 6 days ago by • 0 • written 10 months ago by • 0
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1
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95
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 22 days ago by 65k • written 22 days ago by • 0
3
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5
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597
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
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5
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1.3k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
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199
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 weeks ago Abril • 0
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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
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3
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318
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
12 weeks ago • updated 11 weeks ago island • 0
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2
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248
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
12 weeks ago Diana • 0
0
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1
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267
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
5
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6
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526
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
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2
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645
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago • updated 3 months ago Levi • 0
1
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1
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385
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
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2
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318
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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
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319
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
1
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7
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808
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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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417
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
1
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1
reply
318
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Differential gene expression analysis
RNASeqData RNAseq123
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
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3
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665
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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
3
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4
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516
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
2
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2
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388
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
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1
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324
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 5 months ago by 41k • written 5 months ago by ▴ 10
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358
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 5 months ago by ★ 13k • written 5 months ago by • 0
22
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15
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7.4k
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
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2
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423
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
5 months ago Ben • 0
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2
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628
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MA plot for DESEq2 analysis
RNASeqData DESeq2
5 months ago RHEA • 0
2
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3
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760
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 6 months ago by ★ 1.3k • written 6 months ago by • 0
1
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1
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398
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Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
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1
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388
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 6 months ago by ▴ 780 • written 6 months ago by • 0
2
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4
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647
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
6 months ago Shihui • 0
0
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4
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643
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 10
3
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3
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1.2k
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
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1
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638
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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
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2
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497
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
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0
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320
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How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
7 months ago adi.rotem • 0
1
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1
reply
437
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
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1
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491
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
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491
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Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
2
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3
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1.0k
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bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
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2
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994
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
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2
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826
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DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
8 months ago Marina • 0
1
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2
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1.4k
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IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 8 months ago by ▴ 120 • written 9 months ago by ▴ 10
0
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6
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756
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
1
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2
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501
views
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 9 months ago by 41k • written 9 months ago by • 0
0
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0
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319
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
9 months ago sonal • 0
1
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9
replies
862
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DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
0
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0
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521
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News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
9 months ago info ▴ 10
0
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1
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484
views
DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
1
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1
reply
442
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
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1
reply
658
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 9 months ago by 65k • written 9 months ago by • 0
50 results • Page 1 of 1
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Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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