0
votes
0
replies
6
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData ExperimentHubData
2 hours ago Edward • 0
0
votes
2
replies
51
views
pathview - multiple states
pathview Pathways KEGG
7 hours ago • updated 6 hours ago Philippine • 0
0
votes
5
replies
234
views
fail to use addPerROIQC in Rmd
stand standR
updated 1 day ago by • 0 • written 1 day ago by • 0
0
votes
0
replies
29
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
1 day ago xiaofeiwang198266 • 0
0
votes
1
reply
86
views
rrvgo::calculateSimMatrix() error
rrvgo
updated 2 days ago by • 0 • written 5 days ago by • 0
0
votes
0
replies
49
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
8 days ago David R ▴ 90
0
votes
1
reply
104
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 11 days ago by ★ 4.6k • written 11 days ago by • 0
0
votes
1
reply
110
views
eRNAs count
RNASeq DESeq2
updated 15 days ago by ★ 4.6k • written 15 days ago by • 0
0
votes
0
replies
107
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WGCNA module preservation using only adjacency matrix
WGCNA
20 days ago yang1641 • 0
0
votes
0
replies
56
views
ChemmineOB avaiable for macOS Binary (arm64)?
ChemmineOB
20 days ago Simone • 0
0
votes
2
replies
288
views
installation error for BiocNeighbors package
BiocNeighbors
20 days ago 育 • 0
0
votes
0
replies
103
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP ChAMPdata
22 days ago elgomez • 0
1
vote
3
replies
384
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
25 days ago • updated 5 days ago abadgerw • 0
0
votes
5
replies
542
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
25 days ago • updated 1 day ago abadgerw • 0
0
votes
0
replies
124
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
28 days ago user_bioinfo • 0
0
votes
0
replies
127
views
Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
29 days ago kim • 0
0
votes
0
replies
112
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
29 days ago daccar98 • 0
0
votes
0
replies
131
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
29 days ago brayas13 • 0
0
votes
0
replies
112
views
export processed data from flowploidy
flowPloidy
4 weeks ago Zdenek Skala • 0
0
votes
0
replies
72
views
Filtering Steps for proActiv Analysis
Transcriptomics proActiv
5 weeks ago LuciaNhu • 0
0
votes
0
replies
109
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diffbind covariates
DiffBind ATACSeq
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 220
0
votes
0
replies
82
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
5 weeks ago mario_de_manner • 0
0
votes
0
replies
81
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
6 weeks ago Ibrahim • 0
0
votes
0
replies
88
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DiffBind subset replicates
DiffBind
7 weeks ago Haiping • 0
0
votes
0
replies
117
views
Rsubread - sublong function
pacbio sublong Rsubread
7 weeks ago thomas.heigl.ibk • 0
0
votes
0
replies
110
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when FOLD>0, which group of sampls increased?
BASiCS
7 weeks ago Jeffcgen2000 • 0
0
votes
0
replies
119
views
Paired splsda
mixOmics
7 weeks ago michelafrancesconi8 • 0
0
votes
0
replies
145
views
Background normalization of Diffbind dba.normalize
Normalization DiffBind
7 weeks ago Young Boqin • 0
0
votes
0
replies
152
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DMRcate pcutoff setting
EpicV2 DMRcate
8 weeks ago kitzhu • 0
0
votes
0
replies
154
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[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
8 weeks ago Anke • 0
1
vote
1
reply
301
views
WGCNA
DEGselection RNASeqData WGCNA
updated 8 weeks ago by ▴ 760 • written 8 weeks ago by • 0
0
votes
1
reply
188
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel ChIPQC
written 8 weeks ago by • 0
2
votes
6
replies
864
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miRTarRnaseq library
miRNATarget mirTarRnaSeq
8 months ago • updated 8 weeks ago María Calvo • 0
0
votes
0
replies
149
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Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage Gviz sashimi
8 weeks ago Marco • 0
1
vote
1
reply
238
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
1
vote
1
reply
593
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Convert HGVS Representation back to Reference Genome Coordinates
GA4GHclient
updated 8 weeks ago by ▴ 160 • written 9 weeks ago by ★ 1.5k
0
votes
0
replies
218
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
9 weeks ago tim.meese • 0
0
votes
1
reply
279
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BiomaRt - improved access to Ensembl ?
biomaRt
updated 9 weeks ago by ★ 6.6k • written 9 weeks ago by • 0
0
votes
0
replies
173
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Deprecated Gates- tailgate
openCyto
9 weeks ago ztflaten • 0
0
votes
0
replies
179
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Getting error while running GenomicPlot
GenomicPlot
9 weeks ago Lucky • 0
0
votes
0
replies
187
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
10 weeks ago Fernanda • 0
0
votes
0
replies
162
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package rpx, unable to download any dataset (PRIDE, MassIVE, iProX)
rpx PXDataset RforProteomics
10 weeks ago Jane_Huang • 0
0
votes
0
replies
307
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Generating Boxplots for Gene Expression by CellType in NanoStringGeoMXSet
GeomxTools SpatialDecon GeoMxWorkflows
10 weeks ago Cinque • 0
0
votes
0
replies
208
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
11 weeks ago Alejandro • 0
0
votes
0
replies
264
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modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
11 weeks ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
261
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Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
11 weeks ago Ragnhild • 0
0
votes
1
reply
550
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Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 10 weeks ago by ▴ 60 • written 11 weeks ago by • 0
0
votes
1
reply
272
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 11 weeks ago by ▴ 760 • written 11 weeks ago by • 0
0
votes
5
replies
706
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Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 8 weeks ago by ▴ 450 • written 11 weeks ago by • 0
0
votes
2
replies
400
views
concentration tables suitable as input for new packages?
Bioconductor
12 weeks ago katja.danielzik • 0
1,000 results • Page 1 of 20
Recent ...
Replies
Comment: lfcShrink and alpha value by cropero • 0
Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…
Comment: pathview - multiple states by Philippine • 0
Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…
Comment: pathview - multiple states by Guido Hooiveld ★ 4.1k
A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Adam • 0
Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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