Showing : rnaseq • reset
0
votes
2
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181
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 20 hours ago by ★ 4.6k • written 5 days ago by • 0
1
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5
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362
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Deseq2 Design
RNASeq DESeq2
updated 1 day ago by 67k • written 5 days ago by • 0
0
votes
2
replies
418
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 days ago by 52k • written 12 days ago by ▴ 10
0
votes
1
reply
143
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 25 days ago by ★ 4.6k • written 25 days ago by • 0
0
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4
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292
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 22 days ago by ★ 3.4k • written 29 days ago by • 0
0
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1
reply
133
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eRNAs count
RNASeq DESeq2
updated 29 days ago by ★ 4.6k • written 29 days ago by • 0
1
vote
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
0
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0
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143
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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
votes
11
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753
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 10 weeks ago by • 0
2
votes
4
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426
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
10 weeks ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
306
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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472
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 11 weeks ago by 43k • written 12 weeks ago by ▴ 10
0
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3
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401
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
11 weeks ago Travis • 0
0
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5
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1.7k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.6 years ago by • 0
0
votes
2
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908
views
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
votes
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
votes
3
replies
546
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
4 months ago BioinfGuru ▴ 70
3
votes
6
replies
818
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 4 months ago by • 0
4
votes
3
replies
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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582
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 4 months ago by ★ 4.6k • written 4 months ago by • 0
1
vote
4
replies
1.4k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
5 months ago • updated 4 months ago Lucy ▴ 60
0
votes
4
replies
590
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 5 months ago by • 0
0
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0
replies
344
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
5 months ago JG13 • 0
0
votes
1
reply
377
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 6 months ago by 67k • written 6 months ago by • 0
1
vote
9
replies
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
vote
3
replies
570
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
votes
2
replies
637
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
6 months ago atan • 0
3
votes
2
replies
677
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
7 months ago mohammedtoufiq91 ▴ 10
0
votes
0
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301
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
7 months ago Bibi • 0
10
votes
11
replies
2.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 6 months ago by • 0 • written 7.3 years ago by ▴ 80
1
vote
3
replies
654
views
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
votes
3
replies
796
views
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
votes
1
reply
513
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 months ago by 43k • written 7 months ago by • 0
0
votes
2
replies
454
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 7 months ago by • 0
0
votes
2
replies
600
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
8 months ago • updated 7 months ago catv • 0
5
votes
3
replies
918
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 months ago by 52k • written 8 months ago by • 0
0
votes
1
reply
612
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
532
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
votes
2
replies
1.0k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
9 months ago kcarey • 0
2
votes
2
replies
528
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 months ago Sabiha ▴ 20
0
votes
2
replies
1.3k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 months ago kcarey • 0
1
vote
4
replies
563
views
DESeq2 Replicates
DESeq2 RNASeq
9 months ago kcarey • 0
1
vote
3
replies
687
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
0
votes
4
replies
677
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
776
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 9 months ago by ▴ 10
2
votes
1
reply
498
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 months ago by 43k • written 9 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
replies
512
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 months ago Abril • 0
50 results • Page 1 of 1
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Replies
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi @gordonsmyth and @weishi, Firstly, thank you for offering your time to develop the junction quantification module further. This is gre…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Comment: Build error on kunpeng2 Linux aarch64 by martin.grigorov ▴ 10
Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…
Answer: Standardization of rlog transformed counts before PCA by ATpoint ★ 4.6k
I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…
Votes
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
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