Showing : rnaseq • reset
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4
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
updated 4 days ago by ★ 3.6k • written 4 days ago by • 0
2
votes
2
replies
151
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 days ago mohammedtoufiq91 ▴ 10
1
vote
1
reply
205
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 days ago by 66k • written 8 days ago by • 0
0
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0
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63
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
8 days ago Bibi • 0
10
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11
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1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 6 days ago by • 0 • written 6.8 years ago by ▴ 80
1
vote
3
replies
292
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 13 days ago by 50k • written 14 days ago by • 0
0
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3
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250
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 26 days ago by ★ 4.2k • written 26 days ago by • 0
0
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1
reply
177
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
votes
2
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203
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 5 weeks ago by • 0
0
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2
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258
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 weeks ago catv • 0
5
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3
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334
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
141
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
1
reply
161
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 6 weeks ago by ★ 4.2k • written 7 weeks ago by • 0
0
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2
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293
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
9 weeks ago kcarey • 0
2
votes
2
replies
295
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 weeks ago Sabiha ▴ 20
0
votes
2
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341
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 weeks ago kcarey • 0
1
vote
4
replies
344
views
DESeq2 Replicates
DESeq2 RNASeq
11 weeks ago kcarey • 0
1
vote
3
replies
401
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 10
0
votes
4
replies
344
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
3 months ago • updated 12 weeks ago mperalc • 0
0
votes
2
replies
365
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
5
replies
680
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 12 weeks ago by 42k • written 3 months ago by ▴ 10
2
votes
1
reply
282
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
3
votes
6
replies
618
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
3 months ago boczniak767 ▴ 720
0
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0
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252
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
2
votes
2
replies
454
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
4
replies
451
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
371
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
4 months ago • updated 3 months ago island • 0
1
vote
3
replies
645
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 4 months ago by • 0
0
votes
1
reply
269
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 4 months ago by ▴ 210 • written 4 months ago by • 0
2
votes
4
replies
673
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
4
votes
6
replies
662
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
3
votes
1
reply
343
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
0
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3
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583
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
0
votes
1
reply
294
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
1
vote
2
replies
510
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
1
vote
2
replies
478
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
votes
2
replies
900
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
0
votes
3
replies
499
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
6 months ago • updated 5 months ago Karthik • 0
1
vote
1
reply
398
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
2
votes
3
replies
543
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
6 months ago Karthik • 0
2
votes
2
replies
447
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
6 months ago Manthos • 0
2
votes
4
replies
655
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
464
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 6 months ago by 42k • written 7 months ago by • 0
0
votes
2
replies
570
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 6 months ago by ★ 1.1k • written 7 months ago by ▴ 190
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 60
1
vote
4
replies
670
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
0
votes
0
replies
379
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
7 months ago mch • 0
4
votes
2
replies
705
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Error in gseDO function by Javier • 0
Thank you for your answer! The thing is I'm working with 12 genes (I did also some targeted cholesterol efflux-related genes, but for sha…
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by Ali Osman • 0
Thanks for your response and suggestions @atpoint ! I think implementation of the function is not a problem (I already have some options an…
Comment: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU by Marek Gierlinski ▴ 30
Two years on and the issue is still there. Thank you Arthur for the solution!
Comment: Cannot install oligo on Fedora by mbassal • 0
so whats the solution for this error?
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Votes
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
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