Showing : RNASEQ • reset
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 days ago by ★ 4.6k • written 9 days ago by • 0
1
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5
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433
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Deseq2 Design
RNASeq DESeq2
updated 5 days ago by 67k • written 9 days ago by • 0
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2
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426
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 14 days ago by 52k • written 16 days ago by ▴ 10
0
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1
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147
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 29 days ago by ★ 4.6k • written 29 days ago by • 0
0
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4
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304
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 26 days ago by ★ 3.4k • written 4 weeks ago by • 0
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1
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139
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eRNAs count
RNASeq DESeq2
updated 4 weeks ago by ★ 4.6k • written 4 weeks ago by • 0
1
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8
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1.1k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 6 weeks ago by • 0
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0
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146
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
6 weeks ago brayas13 • 0
3
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11
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765
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 10 weeks ago by • 0
2
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4
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434
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
10 weeks ago jihoon.kim.1495 ▴ 10
1
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1
reply
310
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 11 weeks ago by 67k • written 11 weeks ago by • 0
1
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2
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474
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 10
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3
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408
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
12 weeks ago Travis • 0
0
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5
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1.7k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.6 years ago by • 0
0
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2
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912
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
3
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5
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1.0k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 4 months ago by ★ 1.4k • written 4 months ago by • 0
2
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3
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555
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
4 months ago BioinfGuru ▴ 70
3
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6
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819
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 4 months ago by • 0
4
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3
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1.2k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 5 months ago by ▴ 10
0
votes
3
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585
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 5 months ago by ★ 4.6k • written 5 months ago by • 0
1
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4
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1.4k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
5 months ago Lucy ▴ 60
0
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4
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594
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 5 months ago by • 0
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0
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346
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
5 months ago JG13 • 0
0
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1
reply
381
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 6 months ago by 67k • written 6 months ago by • 0
1
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9
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1.5k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 6 months ago by 67k • written 6 months ago by ▴ 10
1
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3
replies
575
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 months ago by 67k • written 6 months ago by ▴ 50
2
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2
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643
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 6 months ago by ▴ 10 • written 7 months ago by • 0
0
votes
6
replies
1.3k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
7 months ago • updated 6 months ago atan • 0
3
votes
2
replies
681
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
7 months ago mohammedtoufiq91 ▴ 10
0
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0
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302
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
7 months ago Bibi • 0
10
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11
replies
2.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 7 months ago by • 0 • written 7.3 years ago by ▴ 80
1
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3
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658
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 months ago by 52k • written 7 months ago by • 0
0
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3
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804
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
0
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1
reply
520
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
0
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2
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458
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 8 months ago by • 0
0
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2
replies
605
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
8 months ago catv • 0
5
votes
3
replies
925
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 months ago by 52k • written 8 months ago by • 0
0
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1
reply
619
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
541
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
0
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2
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1.1k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
9 months ago kcarey • 0
2
votes
2
replies
533
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 months ago Sabiha ▴ 20
0
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2
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1.4k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 months ago kcarey • 0
1
vote
4
replies
568
views
DESeq2 Replicates
DESeq2 RNASeq
9 months ago kcarey • 0
1
vote
3
replies
698
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
0
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4
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681
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 months ago mperalc • 0
0
votes
2
replies
782
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 9 months ago by 52k • written 9 months ago by • 0
3
votes
5
replies
1.1k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 months ago by 43k • written 10 months ago by ▴ 10
2
votes
1
reply
501
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 months ago by 43k • written 10 months ago by ▴ 10
3
votes
6
replies
1.2k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
10 months ago boczniak767 ▴ 740
0
votes
0
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516
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 months ago Abril • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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