Showing : RNAseq • reset
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
6 days ago • updated 3 days ago sindhuri • 0
0
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2
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294
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 28 days ago by ★ 4.6k • written 4 weeks ago by • 0
1
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5
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526
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Deseq2 Design
RNASeq DESeq2
updated 29 days ago by 67k • written 4 weeks ago by • 0
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2
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480
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 5 weeks ago by 52k • written 5 weeks ago by ▴ 10
0
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1
reply
183
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 7 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
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5
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442
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 8 weeks ago by • 0
0
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1
reply
161
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eRNAs count
RNASeq DESeq2
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
1
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8
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1.2k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 10 weeks ago by • 0
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0
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161
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
10 weeks ago brayas13 • 0
3
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11
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804
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
2
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4
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464
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
3 months ago jihoon.kim.1495 ▴ 10
1
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1
reply
377
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 3 months ago by 67k • written 3 months ago by • 0
1
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2
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504
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
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3
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446
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
3 months ago Travis • 0
0
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5
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1.8k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.7 years ago by • 0
0
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2
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952
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 4 months ago by ★ 1.4k • written 4 months ago by • 0
3
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5
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1.1k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
2
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3
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599
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
5 months ago BioinfGuru ▴ 70
3
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6
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856
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 5 months ago by • 0
4
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3
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1.3k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 6 months ago by ▴ 10
0
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3
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610
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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1.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
6 months ago • updated 5 months ago Lucy ▴ 60
0
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4
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628
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
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0
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370
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
6 months ago JG13 • 0
0
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1
reply
398
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 7 months ago by 67k • written 7 months ago by • 0
1
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9
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1.6k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 7 months ago by 67k • written 7 months ago by ▴ 10
1
vote
3
replies
607
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 7 months ago by 67k • written 7 months ago by ▴ 50
2
votes
2
replies
667
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 months ago by ▴ 10 • written 8 months ago by • 0
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6
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1.4k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
7 months ago atan • 0
3
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2
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708
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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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323
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
8 months ago Bibi • 0
10
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11
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2.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 7 months ago by • 0 • written 7.4 years ago by ▴ 80
1
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3
replies
685
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 8 months ago by 52k • written 8 months ago by • 0
0
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3
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856
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
0
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1
reply
553
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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486
views
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
642
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
9 months ago • updated 8 months ago catv • 0
5
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3
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975
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 months ago by 52k • written 9 months ago by • 0
0
votes
1
reply
644
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
1
reply
576
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 months ago by ★ 4.6k • written 9 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
10 months ago • updated 9 months ago kcarey • 0
2
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2
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556
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 months ago Sabiha ▴ 20
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2
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1.5k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 months ago kcarey • 0
1
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4
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588
views
DESeq2 Replicates
DESeq2 RNASeq
10 months ago kcarey • 0
1
vote
3
replies
729
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 10
0
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4
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707
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 months ago mperalc • 0
0
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2
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825
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 10 months ago by 52k • written 10 months ago by • 0
3
votes
5
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1.2k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 10 months ago by ▴ 10
2
votes
1
reply
518
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 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
11 months ago • updated 10 months ago boczniak767 ▴ 740
50 results • Page 1 of 1
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Comment: Differential variability modelling with vst() expression by convincing.shark.jqvy • 0
Your approach to differential variability modeling using vst() looks promising! It mirrors the challenge of mastering levels in [Geometry D…
Answer: DESeq2 Heatmap by James W. MacDonald 67k
Two things. First, `scale` is already vectorized, so you don't have to use `apply`. You can instead just do `t(scale(t(mat)))` . Second, th…
Answer: Improve performance of qusage aggregateGeneSet by James W. MacDonald 67k
This support site is meant mostly to help people with questions about using Bioconductor packages rather than posting code improvements. I …
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Votes
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
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