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128
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
12 days ago • updated 4 days ago
glaciya2018
• 0
0
votes
2
replies
212
views
PCA plot suggestions
DESeq2
PCAtools
updated 10 days ago by
Michael Love
42k • written 12 days ago by
Aaliya
• 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 12 days ago by
Michael Love
42k • written 12 days ago by
kcarey
• 0
0
votes
1
reply
140
views
ATACseq merge peaks
DiffBind
updated 10 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Shloka
• 0
0
votes
0
replies
90
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
12 days ago • updated 8 days ago
Sara
• 0
0
votes
0
replies
85
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
12 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
161
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
13 days ago • updated 12 days ago
ATpoint
★ 4.1k
1
vote
3
replies
216
views
Different Shrunk Log2FC according with reference
DESeq2
updated 12 days ago by
Michael Love
42k • written 13 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
334
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
13 days ago • updated 11 days ago
winwater0928
• 0
2
votes
5
replies
272
views
get BM error
ensembldb
updated 12 days ago by
James W. MacDonald
65k • written 13 days ago by
Fara
• 0
2
votes
5
replies
243
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 11 days ago by
James W. MacDonald
65k • written 13 days ago by
bandconductor
• 0
1
vote
1
reply
179
views
Citation for edgeR user guide
edgeR
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
k___
▴ 30
3
votes
1
reply
315
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
i.sudbery
▴ 40
1
vote
1
reply
114
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
354
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 12 days ago by
swbarnes2
★ 1.3k • written 13 days ago by
Aaliya
• 0
0
votes
0
replies
72
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
13 days ago
info
▴ 10
0
votes
2
replies
249
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
14 days ago • updated 12 days ago
shuwangxinze1996
• 0
0
votes
2
replies
167
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 14 days ago by
taur.vil
• 0
3
votes
3
replies
230
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 days ago by
Michael Love
42k • written 14 days ago by
WardDeb
• 0
1
vote
4
replies
210
views
minfi::read.metharray.exp
minfiData
minfi
updated 13 days ago by
Basti
▴ 780 • written 14 days ago by
clacarion
• 0
1
vote
2
replies
189
views
Improving the design matrices vignette in RNAseq123
RNAseq123
15 days ago • updated 22 hours ago
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
303
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 12 days ago by
James W. MacDonald
65k • written 15 days ago by
Gayatri
• 0
2
votes
13
replies
423
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
15 days ago • updated 12 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
83
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
16 days ago
vaxahey107
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
16 days ago • updated 5 days ago
Chris
• 0
0
votes
0
replies
98
views
I am trying to detect alternative splicing.
ASpli
16 days ago
Sebashish
• 0
3
votes
2
replies
217
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 14 days ago by
Guido Hooiveld
★ 3.9k • written 17 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
127
views
FDR via q-value
qvalue
updated 14 days ago by
James W. MacDonald
65k • written 17 days ago by
John
• 0
0
votes
2
replies
213
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
17 days ago • updated 15 days ago
catv
• 0
0
votes
3
replies
155
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
bas_work
▴ 30
1
vote
0
replies
287
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
17 days ago
BioinfGuru
▴ 30
0
votes
2
replies
137
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
18 days ago
prity6459
• 0
2
votes
2
replies
192
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
sansan
• 0
0
votes
4
replies
204
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
18 days ago
sropri
• 0
1
vote
4
replies
236
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 14 days ago by
James W. MacDonald
65k • written 18 days ago by
Mirella Aurora
• 0
0
votes
3
replies
193
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 18 days ago by
Gordon Smyth
50k • written 18 days ago by
prity6459
• 0
0
votes
0
replies
121
views
Warning while loading DEP package
DEP
updated 18 days ago by
shepherl
3.9k • written 18 days ago by
Namrata
• 0
0
votes
3
replies
171
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 18 days ago by
Alessia
• 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 18 days ago by
Michael Love
42k • written 19 days ago by
ishij9717
• 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 18 days ago by
Michael Love
42k • written 19 days ago by
09191919
• 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 18 days ago by
Gordon Smyth
50k • written 19 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
220
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
19 days ago • updated 18 days ago
Le
• 0
1
vote
2
replies
159
views
Error in champ.load(): The following specified files do not exist
ChAMP
19 days ago • updated 18 days ago
Sherin
• 0
0
votes
1
reply
101
views
Input Question for deseq.r
RSeqAn
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
Nina
• 0
4
votes
6
replies
437
views
FilterByExpr low counts with small sample size
edgeR
19 days ago • updated 14 days ago
Jonathan
▴ 10
0
votes
4
replies
240
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
19 days ago • updated 17 days ago
lonn
• 0
1
vote
2
replies
716
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 days ago • updated 10 days ago
ussarizona
▴ 10
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
quanah.hudson
• 0
0
votes
7
replies
322
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
20 days ago • updated 14 days ago
hortense96
• 0
0
votes
0
replies
84
views
News:
Services
flowBeads
20 days ago
creativepeptides2018
• 0
1,000 results • Page
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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