0
votes
3
replies
190
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 14 days ago by 41k • written 15 days ago by ▴ 20
0
votes
2
replies
186
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
11 days ago • updated 9 days ago catv • 0
3
votes
3
replies
186
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
18 days ago • updated 13 days ago jacques.imbert • 0
1
vote
4
replies
184
views
minfi::read.metharray.exp
minfiData minfi
updated 7 days ago by ▴ 780 • written 8 days ago by • 0
2
votes
2
replies
183
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
18 days ago julia_mcdonough • 0
1
vote
2
replies
182
views
Design Matrix within group comparison more than two groups
DESeq2
18 days ago • updated 17 days ago hemantcnaik • 0
2
votes
2
replies
181
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 25 days ago by ★ 4.1k • written 26 days ago by ★ 1.5k
0
votes
2
replies
180
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
28 days ago • updated 27 days ago Gimena • 0
0
votes
3
replies
179
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 17 hours ago by 65k • written 1 day ago by • 0
1
vote
1
reply
174
views
Differentially expressed genes in monocle pseudotime
monocle
updated 15 days ago by 50k • written 17 days ago by • 0
0
votes
4
replies
173
views
flowStats Search Error
flowStats
updated 14 days ago by 3.8k • written 15 days ago by • 0
3
votes
3
replies
173
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 2 days ago by ★ 4.1k • written 2 days ago by ▴ 10
1
vote
3
replies
172
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 4 days ago by 41k • written 5 days ago by • 0
0
votes
2
replies
172
views
How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
4 weeks ago • updated 29 days ago Seongsu • 0
0
votes
1
reply
171
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 22 days ago by 65k • written 23 days ago by • 0
0
votes
2
replies
170
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 26 days ago Bhawna • 0
0
votes
4
replies
170
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
12 days ago sropri • 0
2
votes
2
replies
167
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 11 days ago by 65k • written 12 days ago by • 0
0
votes
2
replies
166
views
PCA plot suggestions
DESeq2 PCAtools
updated 4 days ago by 41k • written 6 days ago by • 0
0
votes
1
reply
166
views
DESeq2 gives an error and R crashes
DESeq2
20 days ago • updated 19 days ago Shefali • 0
0
votes
3
replies
163
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 12 days ago by 50k • written 12 days ago by • 0
0
votes
1
reply
162
views
Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 29 days ago by 41k • written 4 weeks ago by ▴ 10
2
votes
2
replies
161
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
18 days ago • updated 16 days ago daniel.carbajo • 0
0
votes
2
replies
160
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
28 days ago michelafrancesconi8 • 0
2
votes
2
replies
160
views
[DiffBind] Obtaining normalization factors
DiffBind
18 days ago • updated 15 days ago Henry ▴ 10
1
vote
1
reply
158
views
DESeq2 - Missing values in count matrix
DESeq2
updated 26 days ago by 65k • written 26 days ago by • 0
0
votes
1
reply
154
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 25 days ago by 50k • written 25 days ago by • 0
0
votes
2
replies
153
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 25 days ago by 65k • written 25 days ago by • 0
0
votes
1
reply
153
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 21 days ago by 41k • written 21 days ago by • 0
0
votes
1
reply
152
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 28 days ago by 65k • written 4 weeks ago by • 0
3
votes
1
reply
152
views
Log-cpm values from limma
limma edgeR RNASeq
updated 12 days ago by 50k • written 13 days ago by • 0
0
votes
2
replies
152
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
27 days ago Marianna ▴ 20
1
vote
1
reply
150
views
Citation for edgeR user guide
edgeR
updated 7 days ago by 50k • written 7 days ago by ▴ 30
0
votes
1
reply
148
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 16 days ago by ★ 3.9k • written 20 days ago by • 0
0
votes
3
replies
146
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 18 hours ago by ★ 1.9k • written 12 days ago by • 0
1
vote
2
replies
143
views
Error in champ.load(): The following specified files do not exist
ChAMP
13 days ago • updated 12 days ago Sherin • 0
0
votes
1
reply
143
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 21 days ago by 65k • written 21 days ago by • 0
1
vote
1
reply
143
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
28 days ago Layal • 0
1
vote
1
reply
140
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 5 days ago by 50k • written 9 days ago by ▴ 730
0
votes
1
reply
139
views
Adding columns to DEXSeqResults object
DEXSeq
updated 12 days ago by ★ 1.9k • written 14 days ago by • 0
0
votes
0
replies
138
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
25 days ago andromeda • 0
2
votes
2
replies
138
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
1 day ago Chris • 0
0
votes
0
replies
134
views
Job: PhD-position in bioinformatics / computational biology
Mergeomics Epigenome Evolution NGS Aging
22 days ago arne.sahm • 0
0
votes
1
reply
133
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 15 days ago by • 0 • written 19 days ago by • 0
0
votes
1
reply
133
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 28 days ago by 65k • written 29 days ago by • 0
0
votes
1
reply
133
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 12 days ago by ★ 4.1k • written 13 days ago by • 0
0
votes
1
reply
131
views
SNP locus package for mouse?
SNPlocs packFinder
updated 14 days ago by 65k • written 17 days ago by • 0
0
votes
3
replies
130
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 11 days ago by 65k • written 11 days ago by ▴ 30
0
votes
1
reply
130
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 20 days ago by ★ 4.1k • written 22 days ago by • 0
1
vote
2
replies
129
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
6 days ago ATpoint ★ 4.1k
201 results • Page 3 of 5
Recent ...
Replies
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
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