Showing : RNA-Seq • reset
0
votes
1
reply
1.6k
views
Best way to analyze multiple treatments using DESeq2?
deseq2 rna-seq mirna
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
2
replies
4.4k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 3.6 years ago by • 0 • written 7.6 years ago by • 0
0
votes
0
replies
1.2k
views
How to define the top 100 hub genes in each module and find out the genes having direct connections with hub genes
WGCNA co-expression network RNA-Seq
7.6 years ago wangdp123 • 0
2
votes
1
reply
5.1k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 7.7 years ago by ▴ 1000 • written 7.7 years ago by ▴ 20
1
vote
3
replies
2.1k
views
RNA-seq Batch Correction
rna-seq edger limma removebatcheffect()
updated 7.7 years ago by ★ 29k • written 7.7 years ago by • 0
3
votes
4
replies
3.3k
views
DESeq2 batch effect modeling and matrix not full rank
deseq2 rnaseq rna-seq
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
14
votes
9
replies
4.7k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 7.7 years ago by ▴ 130 • written 9.5 years ago by ▴ 80
2
votes
5
replies
4.4k
views
Analyse only protein_coding genes
bioconductor edger rna-seq
7.7 years ago martin.weihrauch ▴ 20
5
votes
3
replies
2.9k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 6 months ago by ▴ 10 • written 7.8 years ago by ▴ 100
0
votes
0
replies
1.2k
views
Could an experienced user of Polyester help me with some questions?
rna-seq polyester simulation time course
7.8 years ago fa.gholizadeh89 • 0
0
votes
2
replies
2.0k
views
How to simulate a count matrix using Polyester
simulation count matrix RNA-seq Polyester
updated 7.8 years ago by ▴ 210 • written 7.8 years ago by • 0
41
votes
44
replies
14k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 7.8 years ago by ▴ 60 • written 8.4 years ago by ▴ 10
2
votes
2
replies
2.4k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport limma rna-seq
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 60
0
votes
1
reply
3.1k
views
Normalize depth before calculating TPM
rna-seq TPM library size factor
7.9 years ago colore • 0
0
votes
3
replies
2.4k
views
How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2 ruvseq rna-seq batch effect
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
3
votes
3
replies
2.2k
views
How to use limma to do regularization for Ballgown
limma rna-seq
updated 7.9 years ago by ★ 29k • written 7.9 years ago by • 0
5
votes
2
replies
2.5k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
10
votes
9
replies
2.4k
views
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma-voom voom limma rna-seq
updated 7.9 years ago by ★ 29k • written 7.9 years ago by • 0
0
votes
5
replies
2.3k
views
Limma: how to account for twin data (both MZ and DZ twins)?
limma design RNA-seq formula twins
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
3
votes
7
replies
2.5k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2 twins design formula RNA-seq
8.0 years ago Simone • 0
0
votes
1
reply
3.4k
views
How many genes are appropriate for GO enrichment analysis
go annotate rna-seq clusterprofiler
updated 8.0 years ago by ▴ 120 • written 8.0 years ago by ▴ 20
11
votes
3
replies
4.3k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
0
votes
3
replies
1.7k
views
differential splicing events and covariates
limma rna-seq alternative splicing
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 80
0
votes
2
replies
2.6k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 8.0 years ago by ▴ 980 • written 8.0 years ago by ▴ 50
1
vote
2
replies
3.0k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by • 0
5
votes
12
replies
6.8k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 3.9 years ago by ▴ 30 • written 8.0 years ago by ▴ 40
2
votes
5
replies
7.7k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 20
3
votes
4
replies
5.8k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
8.0 years ago David Requena ▴ 20
0
votes
0
replies
1.5k
views
Job: Job: Computational Biologists - Expanding the impact of genomic data on drug development (Immuneering Corporation, Cambridge MA and New York NY)
rna-seq computational biology cns disease gene expression data neurodegeneration Job
8.0 years ago mmartin ▴ 20
3
votes
3
replies
1.3k
views
Saving output from glmTreat to a csv file?
edger rna-seq
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 10
2
votes
0
replies
1.3k
views
p-values, q-values, duplicated entries in output - ballgown
ballgown rna-seq q value r
8.0 years ago mkhasin ▴ 20
3
votes
2
replies
1.8k
views
Bayesian Network analysis of gene regulatory relationship
Bayesian network RNA-seq Gene regulatory network
8.1 years ago nancydong20 ▴ 10
0
votes
0
replies
1.0k
views
Tximport with paired and single ended reads
limma rna-seq bioconductor
8.1 years ago chris86 ▴ 420
1
vote
1
reply
1.8k
views
Does SC3 correct counts for gene length?
sc3 scater single-cell rna-seq biclustering
updated 8.1 years ago by ▴ 150 • written 8.1 years ago by ▴ 20
0
votes
1
reply
3.4k
views
Ballgown Error in file(file, "rt") : invalid 'description' argument
rna-seq ballgown
updated 8.1 years ago by ▴ 210 • written 8.1 years ago by • 0
3
votes
4
replies
6.1k
views
DESeq2 Time course analysis design - only time points WITHOUT treatments
rna-seq deseq2 multiple time points
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
0
votes
1
reply
6.9k
views
Subset data within DeSeq results object
deseq2 R rna-seq
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
1
vote
1
reply
1.3k
views
RNA-seq differential analysis for continuous phenotypes
deseq2 rna-seq
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 70
1
vote
1
reply
1.5k
views
Installing old versions of cummeRbund
rna-seq cummerbund
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
3
votes
3
replies
8.7k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 8.1 years ago by 21k • written 8.1 years ago by ▴ 20
5
votes
4
replies
2.1k
views
Testing for DE genes between samples of isolated cells, accounting for expression in whole tissue
limma rnaseq rna-seq model-matrix multiple factor design
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Cummerbund differential expression data analysis package issue
rna-seq cummerbund
updated 8.2 years ago by 4.2k • written 8.2 years ago by • 0
0
votes
4
replies
3.7k
views
Help with design matrix dealing with 3 variables (DESeq2)
deseq2 rna-seq
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
0
votes
8
replies
3.1k
views
Isoforms detection using bioconductor
bioconductor biomart granges rna-seq
updated 8.2 years ago by ★ 11k • written 8.2 years ago by • 0
3
votes
6
replies
23k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
8.2 years ago nikmehr22 • 0
0
votes
1
reply
1.8k
views
Proper dataset form and model for DEXeq analysis
dexseq rna-seq model.matrix model
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
0
votes
3
replies
2.1k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
deseq2 random effects batch effects RNA-seq rna-seq
written 8.2 years ago by • 0
0
votes
0
replies
1.3k
views
Job: BIOINFORMATICIAN I at Brigham and Women's Hospital, Boston, MA, USA
rna-seq gwas R bioconductor Job
8.3 years ago IV ▴ 30
1
vote
0
replies
2.5k
views
How to test or estimate differential TSS/promoter usage/expression based on RNA-seq data only
tximport differential isoform usage salmon tss rna-seq
8.3 years ago Steffen Heyne ▴ 10
0
votes
2
replies
1.8k
views
Converting Exon counts(co-ordinates) to transcript/gene ids
dexseq bioconductor cancer rna-seq
8.3 years ago Shrule • 0
418 results • Page 6 of 9
Recent ...
Replies
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to Joseph • 0
Popular Question to zhe ▴ 20
Popular Question to Natalia • 0
Locations • All
Seattle, WA, United States, 1 hour ago
Pittsburgh, United States, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
Germany, 3 hours ago
Spain, 4 hours ago
Traffic: 625 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