0
votes
0
replies
9
views
Confidence interval contains 0 but p<0.05
MAST
3 hours ago Adelyn • 0
0
votes
0
replies
19
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData ExperimentHubData
22 hours ago Edward • 0
1
vote
4
replies
216
views
pathview - multiple states
pathview Pathways KEGG
1 day ago • updated 9 hours ago Philippine • 0
0
votes
5
replies
252
views
fail to use addPerROIQC in Rmd
stand standR
updated 1 day ago by • 0 • written 2 days ago by • 0
0
votes
0
replies
33
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
2 days ago xiaofeiwang198266 • 0
0
votes
1
reply
95
views
rrvgo::calculateSimMatrix() error
rrvgo
updated 2 days ago by • 0 • written 6 days ago by • 0
0
votes
0
replies
52
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
9 days ago David R ▴ 90
0
votes
1
reply
108
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 12 days ago by ★ 4.6k • written 12 days ago by • 0
0
votes
1
reply
113
views
eRNAs count
RNASeq DESeq2
updated 16 days ago by ★ 4.6k • written 16 days ago by • 0
0
votes
0
replies
109
views
WGCNA module preservation using only adjacency matrix
WGCNA
20 days ago yang1641 • 0
0
votes
0
replies
57
views
ChemmineOB avaiable for macOS Binary (arm64)?
ChemmineOB
21 days ago Simone • 0
0
votes
2
replies
292
views
installation error for BiocNeighbors package
BiocNeighbors
21 days ago 育 • 0
0
votes
0
replies
106
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP ChAMPdata
23 days ago elgomez • 0
1
vote
3
replies
387
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
25 days ago • updated 6 days ago abadgerw • 0
0
votes
5
replies
550
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
25 days ago • updated 2 days ago abadgerw • 0
0
votes
0
replies
125
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
29 days ago user_bioinfo • 0
0
votes
0
replies
131
views
Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
4 weeks ago kim • 0
0
votes
0
replies
115
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
4 weeks ago daccar98 • 0
0
votes
0
replies
137
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
4 weeks ago brayas13 • 0
0
votes
0
replies
114
views
export processed data from flowploidy
flowPloidy
4 weeks ago Zdenek Skala • 0
0
votes
0
replies
75
views
Filtering Steps for proActiv Analysis
Transcriptomics proActiv
5 weeks ago LuciaNhu • 0
0
votes
0
replies
112
views
diffbind covariates
DiffBind ATACSeq
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 220
0
votes
0
replies
83
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
5 weeks ago mario_de_manner • 0
0
votes
0
replies
82
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
6 weeks ago Ibrahim • 0
0
votes
0
replies
91
views
DiffBind subset replicates
DiffBind
7 weeks ago Haiping • 0
0
votes
0
replies
121
views
Rsubread - sublong function
pacbio sublong Rsubread
7 weeks ago thomas.heigl.ibk • 0
0
votes
0
replies
113
views
when FOLD>0, which group of sampls increased?
BASiCS
7 weeks ago Jeffcgen2000 • 0
0
votes
0
replies
121
views
Paired splsda
mixOmics
7 weeks ago michelafrancesconi8 • 0
0
votes
0
replies
147
views
Background normalization of Diffbind dba.normalize
Normalization DiffBind
8 weeks ago Young Boqin • 0
0
votes
0
replies
152
views
DMRcate pcutoff setting
EpicV2 DMRcate
8 weeks ago kitzhu • 0
0
votes
0
replies
155
views
[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
305
views
WGCNA
DEGselection RNASeqData WGCNA
updated 8 weeks ago by ▴ 760 • written 8 weeks ago by • 0
0
votes
1
reply
189
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel ChIPQC
written 8 weeks ago by • 0
2
votes
6
replies
866
views
miRTarRnaseq library
miRNATarget mirTarRnaSeq
8 months ago • updated 8 weeks ago María Calvo • 0
0
votes
0
replies
153
views
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
239
views
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
594
views
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
221
views
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
281
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 9 weeks ago by ★ 6.6k • written 9 weeks ago by • 0
0
votes
0
replies
174
views
Deprecated Gates- tailgate
openCyto
10 weeks ago ztflaten • 0
0
votes
0
replies
182
views
Getting error while running GenomicPlot
GenomicPlot
10 weeks ago Lucky • 0
0
votes
0
replies
188
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
10 weeks ago Fernanda • 0
0
votes
0
replies
164
views
package rpx, unable to download any dataset (PRIDE, MassIVE, iProX)
rpx PXDataset RforProteomics
10 weeks ago Jane_Huang • 0
0
votes
0
replies
309
views
Generating Boxplots for Gene Expression by CellType in NanoStringGeoMXSet
GeomxTools SpatialDecon GeoMxWorkflows
10 weeks ago Cinque • 0
0
votes
0
replies
209
views
Trying to understand basic DiffBind usage
ChIPSeq DiffBind
11 weeks ago Alejandro • 0
0
votes
0
replies
266
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
11 weeks ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
262
views
Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
11 weeks ago Ragnhild • 0
0
votes
1
reply
556
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 11 weeks ago by ▴ 60 • written 11 weeks ago by • 0
0
votes
1
reply
276
views
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
707
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 8 weeks ago by ▴ 450 • written 12 weeks ago by • 0
1,000 results • Page 1 of 20
Recent ...
Replies
Comment: lfcShrink and alpha value by cropero • 0
Thank you for your fast answer, I have everything clear now
Answer: DESeq2 - Comparing Comparisons by James W. MacDonald 67k
Assuming that WC in your equation #2 is different in KD1 subunit1_vs_WC and SCR subunit1_vs_WC, this is just an interaction, and the easies…
Comment: Differential Expression Genes as Independent Variables by James W. MacDonald 67k
An alternative to that is to use the `glmnet` package to fit a regularized regression using all proteins at once.
Comment: Differential Expression Genes as Independent Variables by abadgerw • 0
Thanks. The proposal was not to include all proteins as covariates in one model but to iterate with one protein serving as the independent …
Answer: How to annotate a limma Elist raw class object with an annotation file by James W. MacDonald 67k
Your first step when trying to use a function is to read the help page (`?mapIds`), which will bring this up: ``` Usage: colu…
Votes
A: How to bin a GRanges to small bins
C: How to bin a GRanges to small bins
C: How to bin a GRanges to small bins
A: deseq2 filter the low counts
A: deseq2 filter the low counts
Awards • All
Popular Question to James W. MacDonald 67k
Popular Question to shepherl 4.1k
Scholar to Gordon Smyth 52k
Popular Question to tombate94 • 0
Popular Question to Ou, Jianhong ★ 1.3k
Locations • All
Australia, just now
France, 12 minutes ago
Australia, 16 minutes ago
United States, 25 minutes ago
Seattle, WA, United States, 1 hour ago
Traffic: 577 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