0
votes
1
reply
722
views
error running exp2grn
NewWave
updated 2.3 years ago by ▴ 40 • written 2.4 years ago by • 0
0
votes
2
replies
915
views
Singlecell protein surface (ADT) pseudotime techniques
monocle slingshot
2.3 years ago EspressoKris ▴ 10
0
votes
3
replies
844
views
shinyMethyl - saving the file
shinyMethyl
2.3 years ago dorota.komar • 0
2
votes
4
replies
1.6k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
2.3 years ago Shihui • 0
0
votes
3
replies
1.3k
views
Suggested package missing from Development version of Bioconductor
Devel
updated 2.3 years ago by 4.2k • written 2.3 years ago by • 0
0
votes
0
replies
681
views
mixOmics with Bioconductor classes
mixOmics
2.3 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
888
views
featureCounts error Assertion failed: (NULL == pairer -> bam_margin_table -> appendix2), function SAM_pairer_finish_margin_table, file input-files.c,…
NewWave
2.3 years ago Kilian • 0
0
votes
1
reply
874
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
723
views
HTSeqGenie runs very slow
HTSeqGenie
2.3 years ago zh9118 • 0
0
votes
0
replies
828
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.3 years ago franciscrick41 • 0
5
votes
9
replies
2.9k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 20 months ago by 53k • written 2.3 years ago by ▴ 10
0
votes
5
replies
1.2k
views
DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2.3 years ago Rockbar • 0
0
votes
2
replies
2.4k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
1
reply
1.1k
views
Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
0
votes
1
reply
813
views
Specifying evidence channels in STRINGdb
STRINGdb stringdb
2.3 years ago robynne.braun • 0
0
votes
0
replies
1.3k
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
2.3 years ago Bogdan ▴ 670
0
votes
3
replies
1.0k
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE DESeq2
2.3 years ago ruba-mahmoud • 0
2
votes
2
replies
927
views
Remove duplicates of colData in TreeSummarizedExperiment
dplyr TreeSummarizedExperiment
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
5
replies
1.3k
views
DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
0
votes
2
replies
765
views
Adding chromosome numbers to the respective gene ids of DESeq2 output file
NewWave hgu133a2.db
updated 6 weeks ago by • 0 • written 2.3 years ago by • 0
5
votes
6
replies
1.5k
views
DataFrame Construction With Non-standard Column
S4Vectors
updated 2.3 years ago by 16k • written 2.3 years ago by ★ 1.6k
0
votes
0
replies
861
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
2.3 years ago kthapa • 0
0
votes
1
reply
853
views
''Model_Matrix'' error
DifferentialExpression limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
0
votes
2
replies
5.0k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.5 years ago by ▴ 80
1
vote
3
replies
2.5k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 5.8 years ago by • 0
1
vote
3
replies
4.2k
views
SRAdb: Error downloading sqlite files
sradb
written 8.2 years ago by • 0
2
votes
2
replies
2.1k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 5.1 years ago by ★ 1.6k
0
votes
4
replies
2.9k
views
how to save subsetted GDS file
gwastools
written 7.7 years ago by ▴ 30
0
votes
1
reply
12k
views
heatmap.2 - change column & row locations; angle / rotate
Cancer Cancer
written 12.1 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Rgraphviz installation: DLL problem?
Rgraphviz Rgraphviz
written 15.9 years ago by ▴ 10
1
vote
6
replies
3.8k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 9.1 years ago by ▴ 10
1
vote
0
replies
1.7k
views
News: Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
db0 release Annotation
2.3 years ago kayla.interdonato ▴ 160
0
votes
0
replies
578
views
Huge effect of a single sample on DEGs
limma
2.3 years ago Jonathan ▴ 10
0
votes
4
replies
1.5k
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
1
vote
1
reply
943
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
GEOmetadb GEOmetadb.sqlite dbConnect
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
3
votes
4
replies
1.8k
views
DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
2.3 years ago Jitendra ▴ 10
1
vote
1
reply
807
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
1
vote
6
replies
1.6k
views
DelayedArray::read_sparse_block
DelayedArray
updated 2.3 years ago by 16k • written 2.4 years ago by ▴ 10
1
vote
5
replies
1.3k
views
Manual creation of qPCRset does not work
bug nondetects HTqPCR
updated 2.2 years ago by • 0 • written 2.3 years ago by ▴ 230
0
votes
3
replies
875
views
ukb Chromosomal position information was converted into SNPS
SNPediaR
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
vote
3
replies
1.6k
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 11 months ago by 68k • written 2.3 years ago by • 0
1
vote
4
replies
1.4k
views
MDS plot edgeR
edgeR
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
0
votes
10
replies
2.0k
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware ensembldb
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
2
replies
2.9k
views
Bioconductor version cannot be validated
Bioconductor
updated 2.2 years ago by • 0 • written 2.3 years ago by • 0
0
votes
1
reply
945
views
T.fit function of maSigPro returns error message
maSigPro
2.3 years ago hanna.g • 0
1
vote
1
reply
1.6k
views
What MetaPhlAn3 database was used in cMD 3?
curatedMetagenomicData
updated 2.3 years ago by ★ 1.1k • written 2.3 years ago by • 0
0
votes
4
replies
4.0k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 14 months ago by • 0 • written 2.3 years ago by • 0
0
votes
3
replies
915
views
Technical Replicates in HTqPCR
HTqPCR
written 2.3 years ago by ▴ 230
3
votes
3
replies
1.0k
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
3
votes
3
replies
3.6k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
2.3 years ago Ethan Nguyen • 0
46,706 results • Page 42 of 935
Recent ...
Replies
Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaasocissalpc • 0
Just like attending workshops helps you improve skills in a field, playing 8 Ball Pool helps sharpen your strategy and precision. You can d…
Comment: Upcoming Ensembl API and data access changes - new blog post available by TikTsokaasocissalpc • 0
Thanks for sharing this update. Clear migration timelines and documentation are essential for learners and researchers alike. In healthcare…
Comment: ATACseq rudimentary questions by 4747 • 0
Thank you so much for being detailed, all makes sense now
Answer: How to do differential expresion across time serise with edgeR? by Gordon Smyth 53k
You actually haven't done any DE analysis at all, you've just selected for genes with either zero or large D0 counts. Another issue is tha…
Answer: ATACseq rudimentary questions by Kevin Blighe ★ 4.0k
For differential analysis tools like DiffTF and TOBIAS, the standard and statistically sound approach is to create **one large consensus pe…
Votes
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment?
A: limma-voom duplicateCorrelation once or twice, difference?
A: limma: comparison of repeat measurements - blocking or within-subject correlatio
Answer: DecideTest vs topTAGs in edgeR
A: LIMMA time series spline model.matrix design setup
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to ZheFrench ▴ 60
Popular Question to shepherl 4.2k
Popular Question to Hervé Pagès 16k
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
Australia, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
The city by the bay, 4 hours ago
Spain, 4 hours ago
Pakistan, 5 hours ago
Traffic: 861 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