Showing : rnaseq • reset
1
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4
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3.1k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
19 months ago Lucy ▴ 60
0
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4
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1.2k
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 19 months ago by • 0
0
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0
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828
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
20 months ago JG13 • 0
0
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1
reply
800
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 20 months ago by 68k • written 20 months ago by • 0
1
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9
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4.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 20 months ago by 68k • written 20 months ago by ▴ 10
1
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3
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1.1k
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 20 months ago by 68k • written 20 months ago by ▴ 50
2
votes
2
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1.1k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 21 months ago by ▴ 10 • written 21 months ago by • 0
0
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6
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2.5k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
21 months ago atan • 0
3
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2
replies
1.4k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
21 months ago mohammedtoufiq91 ▴ 10
0
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0
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727
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
21 months ago Bibi • 0
10
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11
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3.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 21 months ago by • 0 • written 8.5 years ago by ▴ 80
1
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3
replies
1.2k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
3
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1.9k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
votes
1
reply
951
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 22 months ago by 43k • written 22 months ago by • 0
0
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2
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871
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 22 months ago by • 0
0
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2
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1.4k
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
22 months ago catv • 0
5
votes
3
replies
1.8k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 21 months ago by 53k • written 22 months ago by • 0
0
votes
1
reply
1.7k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 22 months ago by 43k • written 22 months ago by • 0
0
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1
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1.1k
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
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2
replies
2.4k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
23 months ago kcarey • 0
2
votes
2
replies
939
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
23 months ago Sabiha ▴ 20
0
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2
replies
4.1k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
23 months ago kcarey • 0
1
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4
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1.0k
views
DESeq2 Replicates
DESeq2 RNASeq
24 months ago kcarey • 0
1
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3
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1.2k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 24 months ago by ★ 1.4k • written 24 months ago by ▴ 10
0
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4
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1.1k
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
24 months ago mperalc • 0
0
votes
2
replies
1.3k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 24 months ago by 53k • written 24 months ago by • 0
3
votes
5
replies
1.9k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 24 months ago by 43k • written 2.0 years ago by ▴ 10
2
votes
1
reply
820
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 10
3
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7
replies
2.2k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
2.0 years ago • updated 5 months ago boczniak767 ▴ 740
0
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0
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849
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
2.0 years ago Abril • 0
2
votes
2
replies
1.9k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
2.1 years ago • updated 2.0 years ago jackafiore • 0
1
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2
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2.7k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.8 years ago by • 0
0
votes
4
replies
1.1k
views
Ballgown error in scan for c.tab files
ballgown RNASeq
2.1 years ago candacenewcome • 0
1
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3
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1.3k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
2.1 years ago island • 0
1
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3
replies
1.4k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 2.1 years ago by • 0
0
votes
1
reply
723
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 2.1 years ago by ▴ 220 • written 2.1 years ago by • 0
2
votes
4
replies
3.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
2.1 years ago Sabiha ▴ 20
4
votes
6
replies
1.8k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 2.0 years ago by 53k • written 2.1 years ago by • 0
3
votes
1
reply
968
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
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3
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1.7k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 2.1 years ago by • 0
0
votes
1
reply
911
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
2.1 years ago WS • 0
2
votes
3
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4.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
1
vote
2
replies
1.4k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
2.2 years ago Sabiha ▴ 20
1
vote
2
replies
1.4k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.2 years ago drewhaydensteele • 0
12
votes
5
replies
5.7k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 9 months ago by • 0 • written 2.2 years ago by • 0
0
votes
3
replies
1.4k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.3 years ago • updated 2.2 years ago Karthik • 0
1
vote
1
reply
883
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
2
votes
3
replies
1.7k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
2.3 years ago • updated 2.2 years ago Karthik • 0
2
votes
2
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1.2k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.3 years ago Manthos • 0
2
votes
4
replies
1.6k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.3 years ago Tyler Sagendorf ▴ 10
1,414 results • Page 2 of 29
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Replies
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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