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0
votes
0
replies
979
views
Manually adjusting BCV for exactTest in edgeR based on plotBCV
edgeR
2.7 years ago
f_rahmdani
• 0
0
votes
4
replies
1.8k
views
Unable to install BiocManager
Biocmanager
R
updated 2.7 years ago by
L
▴ 50 • written 2.7 years ago by
sidrah19220
• 0
0
votes
1
reply
571
views
Package requires binary executable from external software?
external
executable
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
t.m.jarva13
• 0
0
votes
0
replies
828
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
2.7 years ago
barrypraveen
• 0
2
votes
2
replies
939
views
How Can I Assess the Reliability of BCV (Square-Root Dispersion) in Non-Replicated Experiments for Differential Expression Analysis Using edgeR?
edgeR
2.7 years ago
f_rahmdani
• 0
1
vote
3
replies
1.3k
views
Recount3 data correspond to TCGA data
recount3
updated 10 months ago by
Leonardo Collado Torres
★ 1.1k • written 2.7 years ago by
kevin lee
• 0
0
votes
1
reply
2.5k
views
biomaRt - NameSpace loading failed
biomaRt
bioma
updated 2.7 years ago by
Mike Smith
★ 6.6k • written 2.7 years ago by
Alessia
• 0
0
votes
0
replies
981
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
2.7 years ago
Levi
• 0
0
votes
3
replies
1.3k
views
BiomaRt: problems annotating a list of DEGs from DESeq2
biomaRt
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
alan.g.hudson
• 0
1
vote
3
replies
2.4k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 2.7 years ago by
Guido Hooiveld
★ 4.1k • written 2.7 years ago by
m-bihie
▴ 10
0
votes
0
replies
405
views
How to set dropout rate using splatSimDropout function of splatter ?
lazappi
2.7 years ago
shamsuzzaman86
• 0
0
votes
0
replies
768
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq
DRIMSeq
2.7 years ago
Luca
• 0
0
votes
0
replies
1.1k
views
Confusing DSS outputs with smoothing (DMLtest)
DSS
2.7 years ago
Weisheng
• 0
0
votes
3
replies
1.2k
views
DRIMseq error for paired sample analysis
DRIMSeq
2.7 years ago
Luca
• 0
0
votes
1
reply
917
views
Error in names(label_color[label_color == "organe"]) <- "lysosome" : 'names' attribute [1] must be the same length as the vector [0]
EnhancedVolcano
updated 2.7 years ago by
elefth.pavlos
▴ 40 • written 2.7 years ago by
Phương Thùy
• 0
0
votes
0
replies
1.2k
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb
AnnotationDbi
Annotation
2.7 years ago
ahiser
• 0
0
votes
2
replies
1.7k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
2.7 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
606
views
Best practice for comparing a subset of data /
DESeq2
2.7 years ago
TzuChiao
▴ 10
0
votes
3
replies
1.4k
views
Annotated dendogram (tree) from tbl_graph
dendogram
ggtreeExtra
ggtree
annotation
Annotation
2.7 years ago
christian.dina
• 0
0
votes
0
replies
962
views
Using a clustree object to draw a "classical" dendogram
ggplot
dendogram
ggtreeExtra
clustree
ggtree
2.7 years ago
christian.dina
• 0
0
votes
1
reply
784
views
HiCDCPlus extract_hic_eigenvectors() only works with larger bin sizes (> =250kb )?
HiCDCPlus
updated 2.5 years ago by
merve.sahn
• 0 • written 2.7 years ago by
mlin18
• 0
0
votes
1
reply
785
views
How to adjust plots generated using psygenet2r?
psygenet2r
updated 2.7 years ago by
helucro
▴ 70 • written 2.7 years ago by
marinaw
▴ 20
0
votes
2
replies
1.1k
views
Doubt about expression data as well as assay
GEOquery
ExpressionData
assay
SummarizedExperiment
ExpressionAtlas
updated 2.7 years ago by
pmadrigal
• 0 • written 2.7 years ago by
Kritikaverma2707
• 0
0
votes
0
replies
843
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.7 years ago
Giulia
• 0
1
vote
1
reply
1.0k
views
FlowSOM with unrelated channels
FlowSOM
cytofWorkflow
updated 2.7 years ago by
helucro
▴ 70 • written 2.7 years ago by
Anirban
• 0
0
votes
0
replies
812
views
Module Trait Corelation
WGCNA
2.7 years ago
allanokwaro
• 0
0
votes
1
reply
1.5k
views
Specific versions of packages
Bioconductor
updated 2.7 years ago by
Mike Smith
★ 6.6k • written 2.7 years ago by
Gábor Csárdi
▴ 90
0
votes
0
replies
746
views
getGEO error when trying to download a series matrix file
getGEOerror
2.7 years ago
suyonj
• 0
0
votes
0
replies
651
views
Align to reference genome
Alignment
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Antonio
• 0
0
votes
1
reply
986
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 2.7 years ago by
Basti
▴ 780 • written 2.7 years ago by
fuqichen1
• 0
0
votes
0
replies
810
views
cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
2.7 years ago
edward.esiribloom
• 0
2
votes
1
reply
5.6k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 2.7 years ago by
RMiller
▴ 20 • written 2.8 years ago by
kevin
• 0
0
votes
0
replies
1.1k
views
Human to mouse SNP conversion
liftOver
SNP
GWASTools
2.8 years ago
bonheur
• 0
0
votes
0
replies
677
views
goMeth
missMethyl
2.8 years ago
anmolanp
▴ 10
0
votes
0
replies
765
views
Limma: Models containing an intercept and interactions with continuous variables.
limma
edgeR
DifferentialExpression
2.8 years ago
Aashil
• 0
0
votes
0
replies
910
views
combat for batch effect correction in EPIC array data
Epigenetics
combat
EPIC
2.8 years ago
Jitendra
▴ 10
0
votes
0
replies
497
views
Determining a delta G for full metabolic pathway changes
deltaG
metabolicmapping
2.8 years ago
chelsea.st.germain
• 0
0
votes
0
replies
749
views
Some questions regarding using limma and interpretation
limma
2.8 years ago
Sep
• 0
0
votes
1
reply
624
views
How to save primers in a local file with openPrimeR
openPrimeR
updated 2.8 years ago by
Basti
▴ 780 • written 2.8 years ago by
Santiago Edilberto
• 0
0
votes
1
reply
2.0k
views
Am I able to add gene names/symbols to an enrichGO() output?
clusterProfiler
enrichplot
updated 2.8 years ago by
Guido Hooiveld
★ 4.1k • written 2.8 years ago by
GenoMexa
• 0
0
votes
0
replies
880
views
rDGIdb package: score of the results
rDGIdb
r
2.8 years ago
HELEN
• 0
0
votes
0
replies
752
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.8 years ago
Ben J
▴ 20
4
votes
2
replies
1.1k
views
A way to find which genome builds a package supports
build
genome
2.8 years ago
Dmitry
• 0
1
vote
9
replies
3.9k
views
conumee with Infinium MethylationEPIC v2.0
MethylationEPICv2.0
conumee
updated 12 months ago by
fraober
• 0 • written 2.8 years ago by
luca.s
▴ 50
0
votes
0
replies
734
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind
MeRIP-seq
m6A-seq
2.8 years ago
zhiyi
• 0
2
votes
1
reply
1.5k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 2.3 years ago by
wrab425
• 0 • written 2.8 years ago by
snijesh
▴ 200
0
votes
0
replies
540
views
DMRcaller Neighborhood method
DMRcaller
2.8 years ago
Sarah
• 0
5
votes
2
replies
2.5k
views
Support for new Illumina human methylation EPIC array v2
human
methylationArrayAnalysis
updated 4 months ago by
hicks
• 0 • written 2.8 years ago by
jenniewoo
▴ 80
0
votes
1
reply
840
views
Definition of disease_subtype abbreviations
curatedMetagenomicData
updated 2.7 years ago by
Lucas Schiffer
▴ 240 • written 2.8 years ago by
Sehyun Oh
▴ 10
0
votes
0
replies
1.3k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
2.8 years ago
Manav
• 0
1,000 results • Page
13 of 20
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Replies
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
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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