Showing : RNASeq • reset
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 13 days ago by ★ 4.6k • written 17 days ago by • 0
1
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5
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470
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Deseq2 Design
RNASeq DESeq2
updated 13 days ago by 67k • written 17 days ago by • 0
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2
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447
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 23 days ago by 52k • written 24 days ago by ▴ 10
0
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1
reply
159
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
0
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4
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318
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 4 weeks ago by ★ 3.4k • written 6 weeks ago by • 0
0
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1
reply
150
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eRNAs count
RNASeq DESeq2
updated 6 weeks ago by ★ 4.6k • written 6 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 7 weeks ago by • 0
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0
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150
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
7 weeks ago brayas13 • 0
3
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11
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784
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 weeks ago by • 0
2
votes
4
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446
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
11 weeks ago jihoon.kim.1495 ▴ 10
1
vote
1
reply
332
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 12 weeks ago by 67k • written 12 weeks ago by • 0
1
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2
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487
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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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422
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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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1.7k
views
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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929
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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
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
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3
replies
568
views
RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
4 months ago BioinfGuru ▴ 70
3
votes
6
replies
828
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 5 months ago by ▴ 10
0
votes
3
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595
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
vote
4
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1.5k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
5 months ago Lucy ▴ 60
0
votes
4
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608
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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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355
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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
388
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 6 months ago by 67k • written 6 months ago by • 0
1
vote
9
replies
1.6k
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
589
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
653
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 months ago by ▴ 10 • written 7 months ago by • 0
0
votes
6
replies
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
votes
2
replies
695
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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310
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 7 months ago by • 0 • written 7.4 years ago by ▴ 80
1
vote
3
replies
670
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
828
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
votes
1
reply
532
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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466
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 8 months ago by • 0
0
votes
2
replies
620
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
8 months ago catv • 0
5
votes
3
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945
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
625
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
551
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
replies
1.1k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
9 months ago kcarey • 0
2
votes
2
replies
543
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
1.4k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 months ago kcarey • 0
1
vote
4
replies
575
views
DESeq2 Replicates
DESeq2 RNASeq
9 months ago kcarey • 0
1
vote
3
replies
714
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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688
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 months ago mperalc • 0
0
votes
2
replies
795
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 10 months ago by 52k • written 10 months ago by • 0
3
votes
5
replies
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
509
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
10 months ago boczniak767 ▴ 740
0
votes
0
replies
519
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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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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