Showing : rnaseq • reset
0
votes
3
replies
135
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 10 hours ago by • 0 • written 6.7 years ago by ▴ 80
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 11 days ago by 41k • written 12 days ago by • 0
0
votes
2
replies
166
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 13 days ago by • 0
0
votes
2
replies
213
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
17 days ago • updated 14 days ago catv • 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma edgeR RNASeq
updated 17 days ago by 50k • written 18 days ago by • 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 18 days ago by 41k • written 18 days ago by • 0
0
votes
1
reply
140
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 26 days ago by ★ 4.1k • written 28 days ago by • 0
0
votes
2
replies
232
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
2
votes
2
replies
264
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
0
votes
2
replies
270
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
1
vote
4
replies
308
views
DESeq2 Replicates
DESeq2 RNASeq
8 weeks ago kcarey • 0
1
vote
3
replies
365
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 weeks ago by ★ 1.3k • written 9 weeks ago by ▴ 10
0
votes
4
replies
304
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago mperalc • 0
0
votes
2
replies
301
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
3
votes
5
replies
633
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 41k • written 10 weeks ago by ▴ 10
2
votes
1
reply
267
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 41k • written 10 weeks ago by ▴ 10
3
votes
6
replies
536
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
11 weeks ago • updated 10 weeks ago boczniak767 ▴ 720
0
votes
0
replies
225
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 weeks ago Abril • 0
2
votes
2
replies
411
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago • updated 12 weeks ago jackafiore • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
4
replies
401
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
339
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
582
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
239
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 200 • written 3 months ago by • 0
2
votes
4
replies
594
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
4
votes
6
replies
604
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
3
votes
1
reply
303
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
3
replies
492
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
votes
1
reply
272
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
2
votes
3
replies
1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
1
vote
2
replies
468
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
2
replies
443
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
votes
2
replies
807
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
460
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
vote
1
reply
377
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
2
votes
3
replies
478
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
2
votes
2
replies
409
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
2
votes
4
replies
610
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
442
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
0
votes
2
replies
540
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 6 months ago by ★ 1.0k • written 6 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 6.5 years ago by ▴ 60
1
vote
4
replies
636
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
356
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
4
votes
2
replies
634
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
0
votes
6
replies
861
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
votes
0
replies
338
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
0
votes
2
replies
643
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago Karthik • 0
0
votes
0
replies
284
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
0
votes
0
replies
340
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset) by Caio • 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
The left plot indicates you should use genome segmentation. It is what is called "nonstationary" meaning it looks like there are distinct r…
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by gene_bioconductor ▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Awards • All
Popular Question to priyanka.m • 0
Popular Question to Vincent J. Carey, Jr. 6.7k
Scholar to ATpoint ★ 4.1k
Popular Question to Ben ▴ 50
Popular Question to Sam ▴ 10
Locations • All
United States, 1 minute ago
India, 2 minutes ago
United States, 3 minutes ago
United States, 5 minutes ago
Brazil, 9 minutes ago
Traffic: 783 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