Showing : RNASeq • reset
2
votes
2
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999
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 17 months ago by ▴ 10 • written 17 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
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
17 months ago mohammedtoufiq91 ▴ 10
0
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0
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633
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
17 months ago Bibi • 0
10
votes
11
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3.1k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 17 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
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1
reply
831
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
2
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776
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 18 months ago by • 0
0
votes
2
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1.2k
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
18 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 18 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 18 months ago by 43k • written 18 months ago by • 0
0
votes
1
reply
975
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
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2.0k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
19 months ago kcarey • 0
2
votes
2
replies
833
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
20 months ago Sabiha ▴ 20
0
votes
2
replies
3.0k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
20 months ago kcarey • 0
1
vote
4
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894
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
1.1k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 20 months ago by 53k • written 20 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 20 months ago by ▴ 10
2
votes
1
reply
731
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
3
votes
7
replies
1.9k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
20 months ago • updated 8 weeks ago boczniak767 ▴ 740
0
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0
replies
753
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
1000
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
replies
1.3k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 21 months ago by • 0
0
votes
1
reply
648
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 21 months ago by ▴ 220 • written 21 months ago by • 0
2
votes
4
replies
2.1k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
21 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
886
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
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1.5k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 22 months ago by • 0
0
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1
reply
795
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 22 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
22 months ago Sabiha ▴ 20
1
vote
2
replies
1.1k
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
23 months ago Karthik • 0
1
vote
1
reply
756
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
2
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3
replies
1.5k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
23 months ago Karthik • 0
2
votes
2
replies
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
23 months ago Manthos • 0
2
votes
4
replies
1.4k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
24 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
796
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 2.0 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 8.0 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
822
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 2.0 years ago by 53k • written 2.0 years ago by ▴ 10
1,409 results • Page 2 of 29
Recent ...
Replies
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be far…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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