Showing : RnaSeq • reset
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Deseq2 Design
RNASeq DESeq2
updated 1 day ago by 67k • written 1 day ago by • 0
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50
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
1 day ago • updated 16 hours ago bbao • 0
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2
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400
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 7 days ago by 52k • written 8 days ago by ▴ 10
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1
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135
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 21 days ago by ★ 4.6k • written 21 days ago by • 0
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4
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288
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 18 days ago by ★ 3.4k • written 25 days ago by • 0
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1
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130
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eRNAs count
RNASeq DESeq2
updated 25 days ago by ★ 4.6k • written 25 days ago by • 0
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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 5 weeks ago by • 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
5 weeks ago brayas13 • 0
3
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11
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746
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 9 weeks ago by • 0
2
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4
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419
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
9 weeks ago jihoon.kim.1495 ▴ 10
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1
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298
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 10 weeks ago by 67k • written 10 weeks ago by • 0
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2
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466
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 10 weeks ago by 43k • written 11 weeks ago by ▴ 10
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3
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399
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
11 weeks ago Travis • 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
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2
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903
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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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985
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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
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3
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538
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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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815
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 4 months ago by • 0
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3
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1.2k
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 4 months ago by ▴ 10
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3
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580
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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
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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 • updated 4 months ago Lucy ▴ 60
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4
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589
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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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341
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
5 months ago JG13 • 0
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1
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373
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 5 months ago by 67k • written 5 months ago by • 0
1
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9
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1.5k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 5 months ago by 67k • written 6 months ago by ▴ 10
1
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3
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568
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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634
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 6 months ago by ▴ 10 • written 6 months ago by • 0
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6
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1.3k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
6 months ago atan • 0
3
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2
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674
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 months ago mohammedtoufiq91 ▴ 10
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299
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
6 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 6 months ago by • 0 • written 7.3 years ago by ▴ 80
1
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3
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651
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
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3
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785
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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
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503
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
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2
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452
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 7 months ago by • 0
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2
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595
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
7 months ago catv • 0
5
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3
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908
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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
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603
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 months ago by 43k • written 8 months ago by • 0
0
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1
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511
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
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2
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1.0k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
8 months ago kcarey • 0
2
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2
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526
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 months ago Sabiha ▴ 20
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2
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1.3k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 months ago kcarey • 0
1
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4
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561
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DESeq2 Replicates
DESeq2 RNASeq
9 months ago kcarey • 0
1
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3
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681
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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673
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 months ago mperalc • 0
0
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2
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772
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 9 months ago by 52k • written 9 months ago by • 0
3
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5
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1.1k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 months ago by 43k • written 9 months ago by ▴ 10
2
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1
reply
497
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 months ago by 43k • written 9 months ago by ▴ 10
3
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6
replies
1.2k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
9 months ago boczniak767 ▴ 740
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0
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509
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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 ...
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Answer: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k
Hi, In version 1.19.4 of `spatialLIBD` @lahuuki re-implemented the `gene_set_enrichment_plot()` function using `ComplexHeatmap::Heatmap(…
Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Maria please read the mirTarRnaSeq paper. In particular, Supplemental Table 2, clarifies all the statistical models, inputs and outputs. If…
Comment: Help using rtracklayer for gene ID extraction by James W. MacDonald 67k
Telling me you can't do something without showing what you tried is not helpful. When posting here, try to put yourself in the shoes of peo…
Comment: miRTarRnaseq library by María Calvo • 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Answer: Need new version : tx2gene.gencode.v47.csv by Guido Hooiveld ★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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