Showing : RnaSeq • reset
2
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2
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1.0k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 17 months ago by ▴ 10 • written 18 months ago by • 0
0
votes
6
replies
2.1k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
18 months ago • updated 17 months ago atan • 0
3
votes
2
replies
1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
18 months ago mohammedtoufiq91 ▴ 10
0
votes
0
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640
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
18 months ago Bibi • 0
10
votes
11
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3.2k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 18 months ago by • 0 • written 8.2 years ago by ▴ 80
1
vote
3
replies
1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 18 months ago by 53k • written 18 months ago by • 0
0
votes
3
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1.4k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
votes
1
reply
842
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
2
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784
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 19 months ago by • 0
0
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2
replies
1.2k
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
19 months ago catv • 0
5
votes
3
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1.5k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 months ago by 53k • written 19 months ago by • 0
0
votes
1
reply
1.2k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
1
reply
983
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
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2
replies
2.0k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
20 months ago kcarey • 0
2
votes
2
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841
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
20 months ago Sabiha ▴ 20
0
votes
2
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3.0k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
20 months ago kcarey • 0
1
vote
4
replies
905
views
DESeq2 Replicates
DESeq2 RNASeq
20 months ago kcarey • 0
1
vote
3
replies
1.1k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 20 months ago by ★ 1.4k • written 20 months ago by ▴ 10
0
votes
4
replies
1.0k
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
20 months ago mperalc • 0
0
votes
2
replies
1.2k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 20 months ago by 53k • written 21 months ago by • 0
3
votes
5
replies
1.7k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 20 months ago by 43k • written 21 months ago by ▴ 10
2
votes
1
reply
737
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
3
votes
7
replies
1.9k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
21 months ago • updated 9 weeks ago boczniak767 ▴ 740
0
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0
replies
761
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
21 months ago Abril • 0
2
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2
replies
1.7k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
21 months ago jackafiore • 0
1
vote
2
replies
2.4k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.5 years ago by • 0
0
votes
4
replies
1.0k
views
Ballgown error in scan for c.tab files
ballgown RNASeq
21 months ago candacenewcome • 0
1
vote
3
replies
1.2k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
21 months ago island • 0
1
vote
3
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1.3k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 22 months ago by • 0
0
votes
1
reply
657
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 22 months ago by ▴ 220 • written 22 months ago by • 0
2
votes
4
replies
2.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
22 months ago Sabiha ▴ 20
4
votes
6
replies
1.6k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 21 months ago by 53k • written 22 months ago by • 0
3
votes
1
reply
895
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 22 months ago by 53k • written 22 months ago by • 0
0
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3
replies
1.5k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 22 months ago by • 0
0
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1
reply
799
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
22 months ago WS • 0
2
votes
3
replies
3.6k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 23 months ago by ★ 1.4k • written 23 months ago by • 0
1
vote
2
replies
1.2k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
23 months ago Sabiha ▴ 20
1
vote
2
replies
1.2k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
23 months ago drewhaydensteele • 0
12
votes
5
replies
5.0k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by • 0 • written 23 months ago by • 0
0
votes
3
replies
1.3k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
24 months ago • updated 23 months ago Karthik • 0
1
vote
1
reply
761
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
2
votes
3
replies
1.5k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
24 months ago Karthik • 0
2
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2
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1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
24 months ago Manthos • 0
2
votes
4
replies
1.4k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.0 years ago Tyler Sagendorf ▴ 10
0
votes
1
reply
807
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
0
votes
2
replies
1.3k
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 2.0 years ago by ★ 1.1k • written 2.1 years ago by ▴ 200
0
votes
9
replies
3.2k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 2.0 years ago by • 0 • written 8.1 years ago by ▴ 60
1
vote
4
replies
1.5k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.0 years ago Wending • 0
0
votes
0
replies
829
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
2.0 years ago mch • 0
5
votes
2
replies
2.2k
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 10
1,409 results • Page 2 of 29
Recent ...
Replies
Comment: Getting a large intercept with DESeq2 by Denise • 0
Hi, Thank you very much, James and Michael, for getting back to me! I noticed the large intercept when plotting the coefficients returned …
Comment: Error installing Seqinfo by shepherl 4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer by shepherl 4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Answer: Error installing Seqinfo by fabio.marroni • 0
I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Votes
Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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