0
votes
1
reply
12
views
putting my own expression data in deseq2
DESeq2
updated 21 minutes ago by ★ 4.1k • written 1 hour ago by • 0
0
votes
0
replies
20
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
3 hours ago Aurora • 0
0
votes
0
replies
14
views
Version 3.15 S4Vectors packages are missing
S4Vectors
6 hours ago bounlu • 0
0
votes
0
replies
11
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
7 hours ago SSSJec • 0
0
votes
0
replies
23
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
14 hours ago Agung • 0
2
votes
2
replies
112
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
16 hours ago • updated 14 hours ago Chris • 0
0
votes
2
replies
103
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
20 hours ago • updated 7 hours ago SSSJec • 0
0
votes
0
replies
31
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
20 hours ago • updated 18 hours ago Chris • 0
3
votes
3
replies
156
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 1 day ago by ★ 4.1k • written 1 day ago by ▴ 10
1
vote
1
reply
93
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 3 days ago by ▴ 40 • written 3 days ago by ★ 1.5k
0
votes
2
replies
154
views
PCA plot suggestions
DESeq2 PCAtools
updated 3 days ago by 41k • written 5 days ago by • 0
1
vote
3
replies
163
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 3 days ago by 41k • written 4 days ago by • 0
0
votes
1
reply
92
views
ATACseq merge peaks
DiffBind
updated 3 days ago by ★ 4.1k • written 5 days ago by • 0
1
vote
1
reply
133
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 4 days ago by 50k • written 8 days ago by ▴ 730
1
vote
7
replies
252
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
4 days ago • updated 3 days ago pl23 • 0
2
votes
9
replies
321
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 4 days ago by 65k • written 4 days ago by • 0
0
votes
0
replies
60
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
5 days ago glaciya2018 • 0
1
vote
2
replies
123
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
6 days ago • updated 5 days ago ATpoint ★ 4.1k
0
votes
1
reply
114
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 5 days ago by 41k • written 5 days ago by • 0
0
votes
0
replies
58
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
5 days ago • updated 1 day ago Sara • 0
2
votes
5
replies
223
views
get BM error
ensembldb
updated 5 days ago by 65k • written 6 days ago by • 0
2
votes
5
replies
201
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 4 days ago by 65k • written 6 days ago by • 0
0
votes
0
replies
61
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
5 days ago Dario Strbenac ★ 1.5k
1
vote
3
replies
185
views
Different Shrunk Log2FC according with reference
DESeq2
updated 5 days ago by 41k • written 6 days ago by ▴ 20
1
vote
4
replies
271
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
6 days ago • updated 4 days ago winwater0928 • 0
3
votes
1
reply
276
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 6 days ago by 41k • written 6 days ago by ▴ 40
1
vote
1
reply
144
views
Citation for edgeR user guide
edgeR
updated 6 days ago by 50k • written 6 days ago by ▴ 30
0
votes
7
replies
666
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
8 weeks ago • updated 6 days ago shepherl 3.8k
1
vote
1
reply
90
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 6 days ago by 65k • written 6 days ago by ▴ 10
0
votes
8
replies
304
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 5 days ago by ★ 1.3k • written 6 days ago by • 0
0
votes
0
replies
48
views
News: Interested in the analysis of Spatial Omics data?
tidySpatialExperiment SpatialExperiment MoleculeExperiment
6 days ago info ▴ 10
1
vote
4
replies
180
views
minfi::read.metharray.exp
minfiData minfi
updated 6 days ago by ▴ 780 • written 7 days ago by • 0
0
votes
2
replies
200
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
7 days ago • updated 5 days ago shuwangxinze1996 • 0
1
vote
2
replies
958
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate Gviz
updated 7 days ago by ▴ 170 • written 14 months ago by ▴ 10
0
votes
1
reply
119
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 7 days ago by 50k • written 7 days ago by • 0
3
votes
3
replies
200
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
1
vote
4
replies
191
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 7 days ago by 65k • written 11 days ago by • 0
0
votes
1
reply
105
views
FDR via q-value
qvalue
updated 7 days ago by 65k • written 10 days ago by • 0
0
votes
5
replies
276
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 5 days ago by 65k • written 8 days ago by • 0
0
votes
2
replies
181
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 days ago • updated 8 days ago catv • 0
0
votes
3
replies
1.2k
views
News: European Bioconductor Conference 2023 planning
Europe Conference EuroBioC Events News
updated 8 days ago by • 0 • written 18 months ago by ▴ 70
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 7 days ago shepherl 3.8k
1
vote
13
replies
350
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
8 days ago • updated 5 days ago fernanda.backsouza ▴ 10
0
votes
0
replies
67
views
Unlocking Potential: NURS FPX Strategies and Insights
levi NURSFPX ragene20sttranscriptcluster.db ssrch
9 days ago vaxahey107 • 0
13
votes
16
replies
1.0k
views
Why p value inconsistent when using different number of pathway score?
limma
updated 10 hours ago by 50k • written 9 days ago by • 0
0
votes
0
replies
84
views
I am trying to detect alternative splicing.
ASpli
9 days ago Sebashish • 0
3
votes
2
replies
190
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 7 days ago by ★ 3.9k • written 10 days ago by ▴ 10
0
votes
3
replies
124
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 10 days ago by 65k • written 10 days ago by ▴ 30
2
votes
2
replies
164
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 10 days ago by 65k • written 11 days ago by • 0
1
vote
0
replies
235
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
10 days ago BioinfGuru ▴ 30
45,590 results • Page 1 of 912
Recent ...
Replies
Comment: putting my own expression data in deseq2 by ATpoint ★ 4.1k
> directly from GEOquery I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your questi…
Comment: Assist me in determining whether the analysis process using the limma package ha by SSSJec • 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score? by Gordon Smyth 50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by Chris • 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by alserg ▴ 260
fgsea doesn't require the presence of deferentially expressed genes, it takes as the input the differential expression-based ranking of all…
Votes
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
Comment: Why p value inconsistent when using different number of pathway score?
Awards • All
Popular Question to Matthew Ritchie ▴ 1000
Scholar to alserg ▴ 260
Popular Question to bioinf ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to Leo Lahti ▴ 40
Locations • All
Sweden, 3 minutes ago
Italy, 6 minutes ago
France, 10 minutes ago
Germany, 17 minutes ago
Portugal, 22 minutes ago
Traffic: 704 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