Showing : Rnaseq • reset
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 18 months ago by 68k • written 18 months ago by ▴ 50
2
votes
2
replies
1.0k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 18 months ago by ▴ 10 • written 19 months ago by • 0
0
votes
6
replies
2.2k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
18 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
replies
655
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
19 months ago Bibi • 0
10
votes
11
replies
3.2k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 18 months ago by • 0 • written 8.3 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 19 months ago by 53k • written 19 months ago by • 0
0
votes
3
replies
1.4k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
votes
1
reply
860
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
replies
807
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 19 months ago by • 0
0
votes
2
replies
1.2k
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
20 months ago • updated 19 months ago catv • 0
5
votes
3
replies
1.6k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 19 months ago by 53k • written 20 months ago by • 0
0
votes
1
reply
1.3k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
1
reply
1.0k
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
votes
2
replies
2.0k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
21 months ago • updated 20 months ago kcarey • 0
2
votes
2
replies
864
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
21 months ago Sabiha ▴ 20
0
votes
2
replies
3.1k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
21 months ago kcarey • 0
1
vote
4
replies
923
views
DESeq2 Replicates
DESeq2 RNASeq
21 months ago kcarey • 0
1
vote
3
replies
1.1k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 21 months ago by ★ 1.4k • written 21 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
21 months ago mperalc • 0
0
votes
2
replies
1.2k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 21 months ago by 53k • written 21 months ago by • 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
votes
1
reply
755
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
22 months ago • updated 3 months ago boczniak767 ▴ 740
0
votes
0
replies
769
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
22 months ago Abril • 0
2
votes
2
replies
1.7k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
22 months ago jackafiore • 0
1
vote
2
replies
2.5k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.6 years ago by • 0
0
votes
4
replies
1.0k
views
Ballgown error in scan for c.tab files
ballgown RNASeq
22 months ago candacenewcome • 0
1
vote
3
replies
1.2k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
22 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 22 months ago by • 0
0
votes
1
reply
673
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
23 months ago • updated 22 months ago Sabiha ▴ 20
4
votes
6
replies
1.7k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 22 months ago by 53k • written 23 months ago by • 0
3
votes
1
reply
923
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 23 months ago by 53k • written 23 months ago by • 0
0
votes
3
replies
1.6k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 23 months ago by • 0
0
votes
1
reply
825
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
23 months ago WS • 0
2
votes
3
replies
3.7k
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 2.0 years ago by • 0
1
vote
2
replies
1.3k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
24 months ago Sabiha ▴ 20
1
vote
2
replies
1.2k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.0 years ago drewhaydensteele • 0
12
votes
5
replies
5.1k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 6 months ago by • 0 • written 2.0 years 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
2.1 years ago • updated 2.0 years ago Karthik • 0
1
vote
1
reply
779
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
2
votes
3
replies
1.5k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
2.1 years ago • updated 2.0 years 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
2.1 years ago Manthos • 0
2
votes
4
replies
1.4k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.1 years ago Tyler Sagendorf ▴ 10
0
votes
1
reply
829
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 2.1 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 2.1 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 2.1 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
2.1 years ago Wending • 0
0
votes
0
replies
844
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
2.1 years ago mch • 0
1,410 results • Page 2 of 29
Recent ...
Replies
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to shepherl 4.2k
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Locations • All
The city by the bay, 12 minutes ago
United States, 26 minutes ago
WEHI, Melbourne, Australia, 27 minutes ago
Russia, 1 hour ago
United States, 2 hours ago
Traffic: 1922 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6