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0
votes
2
replies
86
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
2 days ago • updated 22 hours ago
Sam
▴ 10
0
votes
1
reply
90
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
updated 2 days ago by
gugu
• 0 • written 2 days ago by
BioinfoMug
• 0
0
votes
0
replies
51
views
Exact same results in Diffbind with different normalization methods
DiffBind
2 days ago
red_bricks
▴ 50
0
votes
0
replies
46
views
FELLA plotGraph function won't change the legend
FELLA
3 days ago
yuhang
• 0
0
votes
0
replies
47
views
medips-output
ngsReports
MEDIPS
3 days ago
subhiksha
• 0
0
votes
0
replies
36
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
3 days ago
bocsci11
• 0
0
votes
0
replies
48
views
The graphical interface of FELLA doesn't work
FELLA
3 days ago
yuhang
• 0
0
votes
0
replies
57
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
3 days ago
jean-christophe.helbling
• 0
0
votes
0
replies
71
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
6 days ago
Henry
• 0
0
votes
1
reply
109
views
Rcpp compilation error
Release
Rcpp
updated 6 days ago by
ATpoint
★ 3.9k • written 7 days ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
71
views
Rain error: invalid annotation of time points
rain
7 days ago
mpuli011
• 0
0
votes
0
replies
63
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
7 days ago
Felix
• 0
0
votes
0
replies
79
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
TCGAbiolinks
9 days ago
Giovanni Calice
▴ 160
0
votes
0
replies
86
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
Andrew
• 0
0
votes
0
replies
71
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
10 days ago
chris2.a.white
• 0
0
votes
0
replies
87
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
13 days ago
jk
• 0
0
votes
0
replies
99
views
Can I combine collinear variables into a single value
BatchEffect
limma
14 days ago
Harrsha
• 0
0
votes
0
replies
145
views
Error in set(x, j = name, value = value) : Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please…
ASpli
14 days ago
vipul14
• 0
0
votes
0
replies
72
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
14 days ago
danalvoronov
▴ 10
0
votes
0
replies
96
views
lfcSE
RGSEA
15 days ago
Gordon
• 0
0
votes
4
replies
181
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
16 days ago • updated 14 days ago
mperalc
• 0
1
vote
0
replies
95
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
17 days ago
BioinfoMug
• 0
0
votes
0
replies
105
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
17 days ago
thomas.heigl.ibk
• 0
0
votes
1
reply
198
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 17 days ago by
ATpoint
★ 3.9k • written 20 days ago by
sodiogoes
• 0
0
votes
6
replies
443
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 4 days ago by
qianyi13
• 0 • written 20 days ago by
Pavel
• 0
0
votes
2
replies
239
views
problem in installing the new version of bioconductor
ANCOMBC
updated 20 days ago by
shepherl
3.8k • written 21 days ago by
Maryam
• 0
0
votes
0
replies
125
views
Comparing the effects of a condition over time in two seperate tissues
MAST
22 days ago
Dillon
• 0
0
votes
4
replies
219
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 22 days ago by
shepherl
3.8k • written 22 days ago by
Lucille
• 0
0
votes
3
replies
169
views
problems updating package
TrajectoryGeometry
22 days ago
michael.shapiro
• 0
0
votes
0
replies
134
views
how to solve this error?
ChAMPdata
ChAMP
26 days ago
Meghana
• 0
1
vote
0
replies
146
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
26 days ago
jarod
▴ 30
0
votes
0
replies
113
views
flowAI: flow rare check in R vs FlowJo
flowAI
27 days ago • updated 24 days ago
Olena
• 0
0
votes
0
replies
136
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
27 days ago
mat149
▴ 70
0
votes
0
replies
93
views
GDC slides download
TCGAbiolinks
27 days ago
jain72744
• 0
0
votes
0
replies
132
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
29 days ago
Abril
• 0
0
votes
4
replies
204
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 4 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 4 weeks ago by
tirordep
• 0
0
votes
1
reply
145
views
"Counts" in enrichGO
GSEABase
updated 4 weeks ago by
Tyler Sagendorf
▴ 10 • written 5 weeks ago by
Matthew
• 0
0
votes
1
reply
153
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 5 weeks ago by
ATpoint
★ 3.9k • written 5 weeks ago by
Priya
• 0
2
votes
15
replies
476
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 4 weeks ago by
Michael Love
41k • written 5 weeks ago by
cinzia.spagnoli
• 0
0
votes
0
replies
87
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
5 weeks ago
nilanjanamani88
• 0
1
vote
1
reply
166
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 4 weeks ago by
Robin
• 0 • written 5 weeks ago by
Pez
▴ 10
0
votes
3
replies
251
views
Unable to install clusterProfiler
clusterProfiler
updated 28 days ago by
Perry
• 0 • written 5 weeks ago by
harsh
• 0
0
votes
0
replies
111
views
rain: Error in peakl[[x]] : subscript out of bounds
rain
5 weeks ago
mata
• 0
1
vote
5
replies
285
views
BiomaRt download data error
biomaRt
updated 5 weeks ago by
Mike Smith
★ 6.4k • written 5 weeks ago by
Max Bone
• 0
0
votes
0
replies
114
views
Recount3 error downloading data
recount3
recount
5 weeks ago
Max Bone
• 0
0
votes
0
replies
88
views
addcrispraiscores - crisprverse not working
crisprDesign
5 weeks ago
jimjacob08
• 0
0
votes
0
replies
90
views
Error reading bam files with getCounts after updating R
chromVAR
chrom
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
tsourkas
• 0
0
votes
0
replies
82
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
5 weeks ago
User3088
• 0
1
vote
4
replies
332
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
5 weeks ago
mikat
• 0
0
votes
0
replies
85
views
What is the significance of DMR in DMRcate
DMRcate
5 weeks ago
chuanjiao6
• 0
1,000 results • Page
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Answer: between lane normalization upper quantile
by
Gordon Smyth
50k
You seem to be assuming that you can simply add up the `normalizedCounts` values from `betweenLaneNormalization` to get normalized library …
Comment: gwas power calculation for quantitative traits
by
Olivia
• 0
Greetings, Having encountered a situation where many students use services to write their academic papers, I realized that this can be a pe…
Answer: Fail BiocManager::install(version='3.12')
by
Jiaxin
• 0
Add `force=T` when downgrade Bioconductor. `BiocManager::install("BiocVersion", version = "3.12", force=T)` Or packages like 'BiocVersion…
Comment: DESeq2: subtract effect of an isotope control before comparing to a baseline sam
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Can you give an example with counts that demonstrates what you mean by adjust by or control for?
Comment: Biostrings: read*StringSet() functions leave open file handles
by
Gerhard Thallinger
▴ 180
Thanks, Hervé, for addressing this issue so quickly. However, still only **Biostrings** 2.70.2 seems to be available. Best, Gerhard
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Confused about the CPM and TMM normalization in edgeR
log2 as input in limma
Fail BiocManager::install(version='3.12')
Fail BiocManager::install(version='3.12')
A: readMSData and netCDF files, how to set polarity ?
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