1
vote
0
replies
201
views
News: Nominations for Bioconductor Awards 2024!
Recognition Awards Bioconductor Bioc204
6 weeks ago • updated 17 hours ago shepherl 3.9k
1
vote
2
replies
198
views
Design Matrix within group comparison more than two groups
DESeq2
24 days ago hemantcnaik • 0
2
votes
2
replies
197
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
7 days ago Chris • 0
0
votes
4
replies
195
views
flowStats Search Error
flowStats
updated 20 days ago by 3.9k • written 21 days ago by • 0
2
votes
2
replies
194
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
24 days ago julia_mcdonough • 0
0
votes
3
replies
193
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 18 days ago by 50k • written 18 days ago by • 0
2
votes
2
replies
192
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 17 days ago by 65k • written 18 days ago by • 0
1
vote
2
replies
189
views
Improving the design matrices vignette in RNAseq123
RNAseq123
15 days ago • updated 23 hours ago Lluís Revilla Sancho ▴ 730
1
vote
1
reply
187
views
Differentially expressed genes in monocle pseudotime
monocle
updated 21 days ago by 50k • written 23 days ago by • 0
0
votes
1
reply
180
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 28 days ago by 65k • written 29 days ago by • 0
2
votes
3
replies
179
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 2 days ago by ★ 4.1k • written 3 days ago by • 0
1
vote
1
reply
179
views
Citation for edgeR user guide
edgeR
updated 13 days ago by 50k • written 13 days ago by ▴ 30
3
votes
1
reply
179
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 19 days ago by • 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
26 days ago • updated 25 days ago Shefali • 0
2
votes
2
replies
174
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
25 days ago • updated 22 days ago daniel.carbajo • 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
24 days ago • updated 21 days ago Henry ▴ 10
0
votes
3
replies
171
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by ★ 1.9k • written 19 days ago by • 0
0
votes
2
replies
168
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 14 days ago by • 0
0
votes
1
reply
165
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 27 days ago by 42k • written 27 days ago by • 0
1
vote
2
replies
161
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
13 days ago • updated 12 days ago ATpoint ★ 4.1k
0
votes
1
reply
161
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 22 days ago by ★ 3.9k • written 26 days ago by • 0
2
votes
3
replies
159
views
package goseq seems to be not available on the latest version of R
goseq
updated 1 day ago by 50k • written 3 days ago by ▴ 20
1
vote
2
replies
159
views
Error in champ.load(): The following specified files do not exist
ChAMP
19 days ago • updated 18 days ago Sherin • 0
0
votes
3
replies
159
views
Store output of matchPWM()
biostrings Biostrings
updated 5 days ago by 65k • written 5 days ago by ▴ 70
0
votes
1
reply
156
views
Adding columns to DEXSeqResults object
DEXSeq
updated 18 days ago by ★ 1.9k • written 20 days ago by • 0
0
votes
3
replies
155
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 17 days ago by 65k • written 17 days ago by ▴ 30
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 12 days ago by 42k • written 12 days ago by • 0
0
votes
1
reply
151
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 27 days ago by 65k • written 27 days ago by • 0
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 days ago by ★ 4.1k • written 19 days ago by • 0
0
votes
1
reply
148
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
0
votes
0
replies
148
views
Job: PhD-position in bioinformatics / computational biology
Mergeomics Epigenome Evolution NGS Aging
28 days ago arne.sahm • 0
3
votes
3
replies
147
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 21 hours ago by ★ 3.3k • written 1 day ago by • 0
0
votes
1
reply
145
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 21 days ago by • 0 • written 26 days ago by • 0
1
vote
3
replies
144
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 13 hours ago by 16k • written 1 day ago by • 0
0
votes
1
reply
142
views
SNP locus package for mouse?
SNPlocs packFinder
updated 20 days ago by 65k • written 23 days ago by • 0
0
votes
2
replies
142
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
5 days ago • updated 4 days ago kcarey • 0
1
vote
2
replies
142
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
20 days ago Ana • 0
0
votes
3
replies
141
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
0
votes
1
reply
140
views
ATACseq merge peaks
DiffBind
updated 10 days ago by ★ 4.1k • written 12 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
1
reply
139
views
rlog transformation
DESeq2
updated 18 days ago by 42k • written 19 days ago by • 0
0
votes
2
replies
137
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
18 days ago prity6459 • 0
2
votes
2
replies
135
views
fgsea significant result
fgsea
2 days ago • updated 1 day ago Chris • 0
0
votes
0
replies
135
views
LearnTaxa with custom Silva
DECIPHER LearnTaxa
26 days ago Eryn • 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 18 days ago by 42k • written 20 days ago by • 0
0
votes
1
reply
135
views
Bioinformatics student
Des DESeq2
updated 24 days ago by • 0 • written 24 days ago by • 0
0
votes
1
reply
133
views
Deseq2 Rlog transformation
DESeq2
updated 22 days ago by ★ 4.1k • written 23 days ago by • 0
0
votes
2
replies
132
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
6 days ago • updated 4 days ago Ian D. ▴ 70
1
vote
1
reply
132
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 10 days ago by ▴ 40 • written 11 days ago by ★ 1.5k
0
votes
0
replies
128
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
12 days ago • updated 4 days ago glaciya2018 • 0
199 results • Page 3 of 4
Recent ...
Replies
Answer: Recovering my account credentials on Bioconductor by shepherl 3.9k
As we will need to exchange some information can you please contact me at bioconductorcoreteam@gmail.com and I can better assist you. Che…
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Awards • All
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Teacher to Gordon Smyth 50k
Popular Question to priyanka.m • 0
Locations • All
France, just now
Sweden, 1 minute ago
United States, 3 minutes ago
United Kingdom, 10 minutes ago
UPF, Barcelona, Spain, 11 minutes ago
Traffic: 752 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