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0
replies
1
view
Empty table plot using plotGseaTable()
fgsea
just now
Chris
• 0
0
votes
2
replies
35
views
Store output of matchPWM()
biostrings
Biostrings
3 hours ago • updated 31 minutes ago
mat149
▴ 70
0
votes
1
reply
92
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 5 hours ago by
Michael Love
41k • written 20 hours ago by
HAK
• 0
0
votes
1
reply
40
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
updated 5 hours ago by
James W. MacDonald
65k • written 17 hours ago by
Yveto
• 0
0
votes
0
replies
19
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 hours ago
Ian D.
▴ 70
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 15 hours ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
188
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
SSSJec
• 0
3
votes
4
replies
131
views
Help with error using camera() in limma
CAMERA
limma
1 day ago • updated 22 hours ago
Chris
• 0
1
vote
1
reply
63
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
marcusn
• 0
0
votes
1
reply
61
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Aurora
• 0
0
votes
1
reply
70
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Agung
• 0
0
votes
0
replies
37
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
1 day ago
Maria Doyle
▴ 70
0
votes
1
reply
48
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 1 day ago by
shepherl
3.8k • written 1 day ago by
bounlu
• 0
0
votes
1
reply
62
views
putting my own expression data in deseq2
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
Dev
• 0
2
votes
2
replies
144
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
2 days ago • updated 1 day ago
Chris
• 0
0
votes
3
replies
186
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
0
votes
0
replies
44
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
2 days ago
Chris
• 0
3
votes
3
replies
179
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
bioinf
▴ 10
1
vote
1
reply
101
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 4 days ago by
Leo Lahti
▴ 40 • written 5 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
171
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 6 days ago by
Aaliya
• 0
1
vote
3
replies
176
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 5 days ago by
Michael Love
41k • written 5 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
107
views
ATACseq merge peaks
DiffBind
updated 5 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Shloka
• 0
1
vote
1
reply
143
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 5 days ago by
Gordon Smyth
50k • written 9 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
270
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
6 days ago • updated 5 days ago
pl23
• 0
2
votes
9
replies
333
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
Alexandre
• 0
0
votes
0
replies
72
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
6 days ago
glaciya2018
• 0
1
vote
2
replies
134
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
7 days ago • updated 6 days ago
ATpoint
★ 4.1k
0
votes
1
reply
122
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 6 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
0
votes
0
replies
64
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
7 days ago • updated 2 days ago
Sara
• 0
2
votes
5
replies
231
views
get BM error
ensembldb
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
Fara
• 0
2
votes
5
replies
210
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
bandconductor
• 0
0
votes
0
replies
67
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
7 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
195
views
Different Shrunk Log2FC according with reference
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
285
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 5 days ago
winwater0928
• 0
3
votes
1
reply
285
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
i.sudbery
▴ 40
1
vote
1
reply
156
views
Citation for edgeR user guide
edgeR
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
k___
▴ 30
0
votes
7
replies
678
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 8 days ago
shepherl
3.8k
1
vote
1
reply
99
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
316
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 6 days ago by
swbarnes2
★ 1.3k • written 8 days ago by
Aaliya
• 0
0
votes
0
replies
58
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
8 days ago
info
▴ 10
1
vote
4
replies
187
views
minfi::read.metharray.exp
minfiData
minfi
updated 7 days ago by
Basti
▴ 780 • written 9 days ago by
clacarion
• 0
0
votes
2
replies
224
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
8 days ago • updated 6 days ago
shuwangxinze1996
• 0
1
vote
2
replies
970
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 8 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
129
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
taur.vil
• 0
3
votes
3
replies
207
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
WardDeb
• 0
1
vote
4
replies
207
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 9 days ago by
James W. MacDonald
65k • written 13 days ago by
Mirella Aurora
• 0
0
votes
1
reply
116
views
FDR via q-value
qvalue
updated 9 days ago by
James W. MacDonald
65k • written 12 days ago by
John
• 0
0
votes
5
replies
284
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 7 days ago by
James W. MacDonald
65k • written 9 days ago by
Gayatri
• 0
0
votes
2
replies
191
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
12 days ago • updated 9 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 9 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
202 results • Page
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Comment: Store output of matchPWM()
by
mat149
▴ 70
out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) Error in do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) : '…
Answer: Store output of matchPWM()
by
James W. MacDonald
65k
Something like this? ``` ind <- as.logical(sapply(hitlist, length)) out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) …
Answer: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
James W. MacDonald
65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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