Showing : rnaseq • reset
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
updated 3 days ago by ★ 3.6k • written 4 days ago by • 0
2
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2
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148
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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
201
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 days ago by 66k • written 7 days ago by • 0
0
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0
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60
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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
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 5 days ago by • 0 • written 6.8 years ago by ▴ 80
1
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3
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291
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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248
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 25 days ago by ★ 4.2k • written 26 days ago by • 0
0
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1
reply
177
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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
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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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257
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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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333
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Log-cpm values from limma
limma edgeR RNASeq
updated 17 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
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1
reply
161
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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
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
9 weeks ago kcarey • 0
2
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2
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295
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 weeks ago Sabiha ▴ 20
0
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2
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340
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 weeks ago kcarey • 0
1
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4
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344
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DESeq2 Replicates
DESeq2 RNASeq
11 weeks ago kcarey • 0
1
vote
3
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400
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 10
0
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4
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342
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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
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364
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 3 months ago by 50k • written 3 months ago by • 0
3
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5
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680
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 12 weeks ago by 42k • written 3 months ago by ▴ 10
2
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1
reply
282
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
3
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6
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617
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Average biological replicates in RNA-seq
Mfuzz RNASeq
3 months ago boczniak767 ▴ 720
0
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0
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252
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
2
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2
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454
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
vote
2
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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
370
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
644
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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
671
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
4
votes
6
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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
342
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
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1
reply
294
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
2
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3
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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
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478
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
votes
2
replies
898
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
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541
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
6 months ago Karthik • 0
2
votes
2
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447
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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
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4
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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
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2
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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
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9
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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
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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
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0
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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: 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…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
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