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Views
Votes
0
votes
0
replies
23
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
3 hours ago
Fabian
• 0
0
votes
0
replies
21
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
13 hours ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
17
views
Materials for liposomes
alabaster.schemas
metaMSdata
16 hours ago
bocsciences
• 0
1
vote
3
replies
194
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 3 days ago by
alan.ocallaghan
▴ 150 • written 4 days ago by
Najla Abassi
• 0
0
votes
0
replies
44
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
3 days ago
gshweta95
• 0
2
votes
1
reply
117
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 4 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
enee
▴ 10
0
votes
0
replies
56
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
6 days ago
nromerov
• 0
1
vote
3
replies
181
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 7 days ago by
Marcel Ramos
690 • written 7 days ago by
Astrid Deschênes
• 0
0
votes
0
replies
67
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
8 days ago
mayra.haedo
• 0
0
votes
0
replies
63
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
8 days ago
taylor.witte
• 0
0
votes
0
replies
79
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 days ago
erbrocato
• 0
1
vote
4
replies
184
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
8 days ago
samuel.channon
• 0
0
votes
2
replies
141
views
Visium RNA
metaMSdata
updated 9 days ago by
vvvc360work2
• 0 • written 9 days ago by
Karlison
• 0
1
vote
2
replies
159
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
maximilian.beikirch
• 0
0
votes
0
replies
69
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
9 days ago
BID
• 0
1
vote
3
replies
178
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 21 hours ago by
mercedeh.movassagh
▴ 10 • written 9 days ago by
María
• 0
0
votes
2
replies
146
views
Error in msaFun Cannot open input file. No alignment!
msa
written 9 days ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
136
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 2 days ago by
Guido Hooiveld
★ 3.9k • written 10 days ago by
Julie
• 0
0
votes
1
reply
126
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 11 days ago by
Gordon Smyth
50k • written 13 days ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
175
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
16 days ago • updated 14 days ago
Sam
▴ 10
0
votes
1
reply
165
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 16 days ago by
BioinfoMug
• 0
0
votes
1
reply
143
views
Exact same results in Diffbind with different normalization methods
DiffBind
16 days ago • updated 11 days ago
red_bricks
▴ 50
0
votes
0
replies
101
views
FELLA plotGraph function won't change the legend
FELLA
16 days ago
yuhang
• 0
0
votes
0
replies
100
views
medips-output
ngsReports
MEDIPS
16 days ago
subhiksha
• 0
0
votes
0
replies
96
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
16 days ago
bocsci11
• 0
0
votes
0
replies
86
views
The graphical interface of FELLA doesn't work
FELLA
17 days ago
yuhang
• 0
0
votes
0
replies
94
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
17 days ago
jean-christophe.helbling
• 0
0
votes
0
replies
109
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
20 days ago
Henry
• 0
0
votes
1
reply
152
views
Rcpp compilation error
Release
Rcpp
updated 20 days ago by
ATpoint
★ 4.0k • written 21 days ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
111
views
Rain error: invalid annotation of time points
rain
21 days ago
mpuli011
• 0
0
votes
0
replies
103
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
21 days ago
Felix
• 0
0
votes
0
replies
110
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
23 days ago • updated 9 days ago
Giovanni Calice
▴ 160
0
votes
0
replies
120
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
Andrew
• 0
0
votes
0
replies
84
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
24 days ago
chris2.a.white
• 0
0
votes
0
replies
105
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
27 days ago
jk
• 0
0
votes
0
replies
113
views
Can I combine collinear variables into a single value
BatchEffect
limma
27 days ago
Harrsha
• 0
0
votes
0
replies
170
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
28 days ago
vipul14
• 0
0
votes
0
replies
88
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
28 days ago
danalvoronov
▴ 10
0
votes
0
replies
110
views
lfcSE
RGSEA
29 days ago
Gordon
• 0
0
votes
4
replies
217
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
4 weeks ago • updated 28 days ago
mperalc
• 0
0
votes
6
replies
533
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 17 days ago by
qianyi13
• 0 • written 4 weeks ago by
Pavel
• 0
1
vote
1
reply
189
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 3 days ago by
SamGG
▴ 330 • written 5 weeks ago by
jarod
▴ 30
0
votes
1
reply
125
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 11 days ago by
Simon Pearce
• 0 • written 7 weeks ago by
User3088
• 0
1
vote
1
reply
322
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 24 days ago by
Yang Liao
▴ 380 • written 8 weeks ago by
Joe Marturano
▴ 10
1
vote
2
replies
617
views
gds in GEOmetadb 2023-06-26 version is empty
GEOmetadb
written 8 months ago by
malat1_t
▴ 10
0
votes
1
reply
559
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 9 months ago by
abhisek001
• 0
0
votes
2
replies
523
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 3 days ago by
CHEN
• 0 • written 10 months ago by
Saanchi
• 0
0
votes
1
reply
823
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 27 days ago by
boczniak767
▴ 720 • written 13 months ago by
Kim
• 0
3
votes
1
reply
1.7k
views
TwoSampleMR and ieugwasr
ieugwasr
clumping
TwoSampleMR
updated 13 days ago by
zoheir.alayash
▴ 10 • written 2.0 years ago by
S T
▴ 90
0
votes
1
reply
633
views
gwas power calculation for quantitative traits
power
GWAS
written 2.6 years ago by
rajya82
• 0
52 results • Page
1 of 2
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
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Michael Love
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May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
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Michael Love
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Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
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Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
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