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Views
Votes
3
votes
4
replies
1.2k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
13 months ago
dseauer
• 0
0
votes
2
replies
782
views
installation error for BiocNeighbors package
BiocNeighbors
13 months ago
育
• 0
0
votes
3
replies
781
views
Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
13 months ago
Stefano Mangiola
▴ 40
0
votes
1
reply
628
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 13 months ago by
Guido Hooiveld
★ 4.1k • written 13 months ago by
Najla Abassi
• 0
2
votes
2
replies
1.1k
views
Handling biological replicates in DESeq2
DESeq2
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
sk
• 0
0
votes
0
replies
584
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP
ChAMPdata
13 months ago
elgomez
• 0
0
votes
1
reply
589
views
forgeBSgenomeDataPkgFromNCBI: Error in find_NCBI_assembly_ftp_dir unable to find FTP dir
BSgenomeForge
non-modelorganism
unabletofindFTPdir
updated 13 months ago by
Hervé Pagès
16k • written 13 months ago by
Geetha
• 0
0
votes
3
replies
938
views
ChIPpeakAnno can not load data
genomes
ChIPpeakAnno
written 15 months ago by
文杰
• 0
10
votes
7
replies
2.4k
views
Why in Bioconductor community people rarely upvote questions?
bioconductor
updated 13 months ago by
shepherl
4.2k • written 2.9 years ago by
L
▴ 50
5
votes
3
replies
29k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 7.0 years ago by
aishu.jp
▴ 30
1
vote
3
replies
900
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
13 months ago • updated 12 months ago
abadgerw
• 0
0
votes
5
replies
1.2k
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
13 months ago • updated 12 months ago
abadgerw
• 0
1
vote
6
replies
1.7k
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 13 months ago by
Michael Love
43k • written 13 months ago by
nramakr
▴ 10
2
votes
4
replies
2.6k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR
BatchEffect
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Thili
• 0
1
vote
8
replies
2.6k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 13 months ago by
Adam Marstrand
• 0
0
votes
2
replies
582
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 13 months ago by
ballackselma
• 0
2
votes
7
replies
4.1k
views
Annotation for EPICv2
EpicV2
ChAMPdata
updated 13 months ago by
icecreamlover
• 0 • written 14 months ago by
nurkenber
• 0
0
votes
0
replies
351
views
ChIP peaks comparison
ChIPSeqData
genomes
ChIPSeq
13 months ago
user_bioinfo
• 0
0
votes
2
replies
1.0k
views
GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi
GOstats
13 months ago
GV Yoshikawa
• 0
1
vote
2
replies
1.5k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
13 months ago
Ai
• 0
4
votes
5
replies
1.4k
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
13 months ago
LuciaNhu
• 0
0
votes
0
replies
640
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
13 months ago
kim
• 0
0
votes
0
replies
411
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes
RNASeq
13 months ago
brayas13
• 0
2
votes
3
replies
1.3k
views
featureCounts segmentation fault with large chromosomes
Rsubread
14 months ago • updated 13 months ago
vkkodali
▴ 10
0
votes
1
reply
754
views
Average expression of genes across replicates
DESeq2
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
James
• 0
0
votes
1
reply
957
views
Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Katerina
• 0
0
votes
1
reply
915
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
mairahtkhan
• 0
0
votes
1
reply
927
views
Normalized counts to be used in decoupleR from deseq2 results
decoupleR
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
James
• 0
2
votes
10
replies
2.8k
views
incomplete official symbol mitochondrial genes in org.Hs.eg.db?
org.Hs.eg.db
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Guido Hooiveld
★ 4.1k
0
votes
8
replies
968
views
Why are internal functions in the package manual?
roxygen
methyLImp2
manual
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
anna
• 0
0
votes
0
replies
339
views
export processed data from flowploidy
flowPloidy
13 months ago
Zdenek Skala
• 0
0
votes
1
reply
434
views
edit y axis scale in errBarchart?
ddCt
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
arustagi
• 0
2
votes
2
replies
1.1k
views
Error: 'term_similarity_from_KEGG' not found in simplifyEnrichment package
simplifyEnrichment
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Yifeii.Ge
• 0
1
vote
0
replies
1.4k
views
News:
Bioconductor 3.20 is Released!
Bioconductor
Release
Software
13 months ago
shepherl
4.2k
0
votes
0
replies
438
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
13 months ago
info
▴ 10
0
votes
1
reply
676
views
probe ID search for SNP (plink)
genomes
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
유빈
• 0
2
votes
2
replies
924
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 13 months ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
Asma
• 0
0
votes
11
replies
2.5k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 8 months ago by
Rob
• 0 • written 13 months ago by
Denise
• 0
2
votes
2
replies
1.6k
views
Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
basilisk
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Stefano Mangiola
▴ 40
4
votes
9
replies
3.0k
views
biomaRt rnorvegicus_gene_ensembl not available anymore
Rattus_norvegicus
biomaRt
updated 12 months ago by
James W. MacDonald
68k • written 13 months ago by
Benjamin
▴ 20
0
votes
0
replies
314
views
Filtering Steps for proActiv Analysis
Transcriptomics
proActiv
13 months ago
LuciaNhu
• 0
2
votes
3
replies
1.8k
views
Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE
ReactomePA
13 months ago
Yifeii.Ge
• 0
0
votes
1
reply
566
views
Deseq to output continous sequencing data
DESeq2
updated 14 months ago by
Michael Love
43k • written 14 months ago by
Neha
• 0
1
vote
4
replies
1.4k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
14 months ago • updated 13 months ago
txema.heredia
• 0
3
votes
3
replies
1.6k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 14 months ago by
Satoshi
• 0
0
votes
0
replies
415
views
diffbind covariates
DiffBind
ATACSeq
updated 14 months ago by
Michael Love
43k • written 14 months ago by
Alpesh Querer
▴ 220
0
votes
0
replies
330
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
14 months ago
mario_de_manner
• 0
5
votes
4
replies
3.0k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment
GSVA
ssGSEA
updated 14 months ago by
Tyler Sagendorf
▴ 10 • written 14 months ago by
Bob
▴ 30
0
votes
3
replies
1.1k
views
Its possible to remove annotation names using anno_simple in ComplexHeatmap
ComplexHeatmap
updated 14 months ago by
Tyler Sagendorf
▴ 10 • written 14 months ago by
nromerov
• 0
0
votes
4
replies
1.1k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs
edgeR
RNASeqData
14 months ago
Philippine
• 0
1,000 results • Page
13 of 20
Recent ...
Replies
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ATpoint
★ 5.0k
> and I first used the normalized counts You would not use these normalized counts for PCA as they're not on log2 scale. As such, the feat…
Comment: EuroBioC2026 abstract submission is open!
by
TikTsokaasocissalpc
• 0
Submitting abstracts for EuroBioC2026 can be exciting but organizing ideas is key. A Random Word Generator [visit][1] can help create uniqu…
Comment: DESeq2 on non-RNASeq counts data
by
TikTsokaasocissalpc
• 0
In data analysis, behavior differences based on data type are common. Similarly, Best EDI Software adapts to non-standard transaction volum…
Comment: blockwiseModule crashes in the end and doesn't generate modules
by
gexose2839
• 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA?
by
TikTsokaasocissalpc
• 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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