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0
votes
1
reply
13
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 23 minutes ago by
James W. MacDonald
64k • written 1 hour ago by
Bo
• 0
0
votes
2
replies
34
views
Can't download Bioconductor
BiocVersion
updated 4 hours ago by
ATpoint
★ 3.6k • written 5 hours ago by
paul.lempka02
• 0
0
votes
1
reply
24
views
Inconsistent results in DiffBind
DiffBind
updated 4 hours ago by
ATpoint
★ 3.6k • written 5 hours ago by
Sam
▴ 10
1
vote
1
reply
57
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE
CpG
minfi
CpGinterrogation
updated 6 hours ago by
James W. MacDonald
64k • written 20 hours ago by
kyj2226
• 0
0
votes
1
reply
72
views
autonomics: example("read_somascan", package = "autonomics") fails, but not on Bioc check servers
autonomics
updated 6 hours ago by
Mike Smith
★ 6.2k • written 6 days ago by
Henrik Bengtsson
★ 2.4k
1
vote
11
replies
136
views
Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions
replicates
SmallRNAData
DESeq2
updated 5 hours ago by
Michael Love
41k • written 11 hours ago by
samer
▴ 10
0
votes
1
reply
60
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
4 days ago • updated 10 hours ago
Sam
▴ 10
0
votes
0
replies
22
views
removeBatchEffect with non-linear model fit
limma
DESeq2
11 hours ago • updated 10 hours ago
georgii.vdovin
• 0
2
votes
4
replies
215
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 21 hours ago by
Gordon Smyth
49k • written 2 days ago by
kyj2226
• 0
0
votes
3
replies
140
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip
limma
goana
updated 1 day ago by
SamGG
▴ 320 • written 2 days ago by
samagbeyimodupe
• 0
0
votes
3
replies
2.5k
views
Problems with FLOWAI
flowAI
updated 3 days ago by
Alexander
• 0 • written 2.6 years ago by
msoares
• 0
1
vote
1
reply
107
views
Asses fit of variance prior
limma
updated 2 days ago by
Gordon Smyth
49k • written 3 days ago by
Frederik Ziebell
▴ 20
0
votes
1
reply
118
views
Interaction terms in DESeq2
RNASeqData
RnaSeqSampleSize
DESeq2
updated 3 days ago by
James W. MacDonald
64k • written 3 days ago by
Mimi
• 0
0
votes
0
replies
40
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
updated 3 days ago by
Michael Love
41k • written 3 days ago by
aehall26
• 0
0
votes
2
replies
96
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR
SeuratscRNA
3 days ago
Bine
▴ 20
3
votes
12
replies
1.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
Bioconductor
devel
Devel
5 months ago • updated 4 days ago
shepherl
3.6k
1
vote
2
replies
122
views
WGCNA documentation not available
WGCNA
updated 4 days ago by
ATpoint
★ 3.6k • written 5 days ago by
ramonmassoni
▴ 10
3
votes
2
replies
158
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 4 days ago by
Gordon Smyth
49k • written 6 days ago by
annikagable
• 0
0
votes
1
reply
87
views
biomaRt_getBM_Failed to collect lazy table
getBM
biomaRt
updated 5 days ago by
James W. MacDonald
64k • written 5 days ago by
ai.yaku
• 0
1
vote
2
replies
112
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
5 days ago
ruba-mahmoud
• 0
0
votes
1
reply
95
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 5 days ago by
ATpoint
★ 3.6k • written 5 days ago by
Miquel
• 0
0
votes
1
reply
530
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 5 days ago by
janetdelvalle056
• 0 • written 12 months ago by
pharamac
• 0
0
votes
3
replies
138
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
written 6 days ago by
Sitapriya
• 0
0
votes
6
replies
185
views
rDGIdb package inconsistency with web interface
rDGIdb
6 days ago • updated 8 hours ago
christopherjamessteel1990
• 0
0
votes
2
replies
111
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink
GSEABenchmarkeR
DESeq2
updated 3 days ago by
ATpoint
★ 3.6k • written 6 days ago by
delphine.rossille
• 0
0
votes
0
replies
32
views
Catalyst::cluster function does NOT produce the same results when setting seed
visua
Visualization
CATALYST
6 days ago
elefth.pavlos
▴ 40
0
votes
1
reply
741
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 6 days ago by
Vanatta
• 0 • written 2.0 years ago by
mairah.khan
• 0
1
vote
3
replies
169
views
SingleR annotation of several slots/patients
SingleR
6 days ago
Bine
▴ 20
0
votes
1
reply
85
views
How to read fcs3.2 files
flowCore
updated 6 days ago by
James W. MacDonald
64k • written 6 days ago by
Gabriel
• 0
0
votes
2
replies
108
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 7 days ago by
Stephanie M. Gogarten
▴ 870 • written 7 days ago by
Mindy wang
• 0
0
votes
2
replies
87
views
Java error while running HiCDC overview code
JuicerTools
HiC
HiCDCPlus
Java
Juicer
written 7 days ago by
IsMM
• 0
0
votes
2
replies
157
views
NCBI protein conversion to CDNA and NCBI gene (in R)
convert
updated 7 days ago by
James W. MacDonald
64k • written 8 days ago by
R_Page
• 0
0
votes
3
replies
190
views
How does Deseq2 deal with the row with zero when calculating size factors
DESeq2
written 7 days ago by
jiakang
• 0
1
vote
2
replies
173
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
8 days ago • updated 7 days ago
drewhaydensteele
• 0
0
votes
8
replies
268
views
GOslim missing GO term
GO.db
GOslim
10 days ago • updated 9 days ago
amanda
• 0
0
votes
3
replies
116
views
Obtaining rsIDs with ENSG and variant ID information
rsid
biomaRt
updated 7 days ago by
Robert Castelo
★ 3.0k • written 10 days ago by
bd2000
• 0
8
votes
6
replies
412
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
updated 3 days ago by
Tim Peters
▴ 160 • written 10 days ago by
Daniel E. Weeks
▴ 30
1
vote
2
replies
115
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 9 days ago by
Gordon Smyth
49k • written 11 days ago by
Jurgen
• 0
3
votes
2
replies
187
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 10 days ago by
Gordon Smyth
49k • written 11 days ago by
annikagable
• 0
2
votes
3
replies
223
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio
cDNA
ensembldb
NCBI
11 days ago • updated 8 days ago
R_Page
• 0
1
vote
1
reply
119
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 11 days ago by
ATpoint
★ 3.6k • written 11 days ago by
kaurprab
• 0
0
votes
7
replies
252
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 11 days ago by
Basti
▴ 740 • written 11 days ago by
486342583
• 0
0
votes
3
replies
221
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 11 days ago by
Guido Hooiveld
★ 3.8k • written 11 days ago by
Aastha Kapoor
• 0
0
votes
1
reply
64
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 11 days ago by
ary.lech
▴ 10
0
votes
0
replies
49
views
Rgraphviz - exported (toFile) dot file loses colour and label information
Rgraphviz
11 days ago
sterlinggunn01
• 0
0
votes
3
replies
156
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 5 days ago by
Ou, Jianhong
★ 1.3k • written 12 days ago by
jfmay
• 0
0
votes
1
reply
136
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
updated 12 days ago by
James W. MacDonald
64k • written 12 days ago by
Levi
• 0
0
votes
0
replies
70
views
multipollutant models
statistics
Regression
r
limma
12 days ago
Jitendra
▴ 10
1
vote
1
reply
110
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 12 days ago by
Robert Castelo
★ 3.0k • written 12 days ago by
snijesh
▴ 20
1
vote
0
replies
55
views
Attempting to import SBML file using R
SBMLR
sbml
rsbm
rsbml
updated 7 days ago by
Michael Love
41k • written 12 days ago by
isasg
▴ 10
45,041 results • Page
1 of 901
Recent ...
Replies
Answer: Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DE
by
James W. MacDonald
64k
The short answer is that you don't. `tximport` is meant to summarize transcript abundance estimates at the gene level, and as you might ima…
Comment: Inconsistent results in DiffBind
by
ATpoint
★ 3.6k
One is the "raw" logFCs, not corrected for the standard error of the logFCs, the other one the shrunken logFCs from DESeq2 lfcShrink, "corr…
Answer: Can't download Bioconductor
by
James W. MacDonald
64k
[You need to update][1]. [1]: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#basic-use
Comment: Can't download Bioconductor
by
ATpoint
★ 3.6k
Please see especially the 1st and 2nd point in https://www.bioconductor.org/help/support/posting-guide/#keypoints
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
Michael Love
41k
With 3 vs 3, when one sample increases from 50 to 5000, this can lead to rejection of null hypothesis. I'm not surprised with the above cou…
Votes
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)
Answer: WGCNA documentation not available
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Comment: Can the limma package be applied to Log2 RUV-normalized data?
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