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4
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meffil.snp.concordance
MethylationArray
methylationArrayAnalysis
MethylationArrayData
meffil
methylation
22 minutes ago • updated 20 minutes ago
kyj2226
• 0
0
votes
0
replies
8
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
2 hours ago
e1271094
• 0
0
votes
0
replies
15
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 hours ago
Dinesh
• 0
0
votes
0
replies
56
views
dba.plotProfile() plotting and interpretation
DiffBind
3 days ago
Henry
▴ 10
0
votes
0
replies
54
views
flowStats for CyTOF
flowStats
4 days ago
tholmes
• 0
0
votes
0
replies
50
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
4 days ago
yvonneh
• 0
0
votes
0
replies
45
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
4 days ago
Ian D.
▴ 70
0
votes
3
replies
140
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 days ago by
ATpoint
★ 4.1k • written 5 days ago by
james.zhang20
• 0
0
votes
0
replies
93
views
Empty table plot using plotGseaTable()
fgsea
5 days ago • updated 3 days ago
Chris
• 0
0
votes
0
replies
76
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
7 days ago
Chris
• 0
0
votes
0
replies
128
views
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
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
0
votes
8
replies
351
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
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
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
0
votes
0
replies
98
views
I am trying to detect alternative splicing.
ASpli
16 days ago
Sebashish
• 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
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
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
0
votes
0
replies
81
views
Enzyme Engineering
BioTIP
19 days ago
bocchemistry
• 0
0
votes
0
replies
94
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
20 days ago
Maliha Tabassum
• 0
0
votes
1
reply
121
views
what is the sampleFiles
chipseq
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
zhulin
• 0
0
votes
0
replies
96
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
21 days ago
Virangika
• 0
0
votes
0
replies
72
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
21 days ago
Henry
▴ 10
0
votes
1
reply
133
views
Deseq2 Rlog transformation
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Sahar
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
24 days ago • updated 21 days ago
Henry
▴ 10
0
votes
3
replies
257
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 18 days ago by
W. Evan Johnson
▴ 850 • written 25 days ago by
schlumbohm
• 0
0
votes
0
replies
92
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
25 days ago
Stevie Pederson
• 0
3
votes
6
replies
277
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
25 days ago
nhaus
▴ 30
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
26 days ago • updated 25 days ago
Shefali
• 0
0
votes
0
replies
135
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
26 days ago
Eryn
• 0
0
votes
0
replies
87
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
26 days ago
Dennis
• 0
0
votes
1
reply
161
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 22 days ago by
Guido Hooiveld
★ 3.9k • written 26 days ago by
Lucie
• 0
0
votes
0
replies
112
views
ggtree tip label position (depth)
ggtree
27 days ago
Roope
• 0
2
votes
6
replies
404
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
28 days ago
Chris
• 0
0
votes
0
replies
150
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
4 weeks ago
andromeda
• 0
0
votes
1
reply
135
views
Granges regionCounts not returning the expected number of entries
methylKit
4 weeks ago
Modoc Kesner
▴ 10
0
votes
0
replies
104
views
flowDensity on a flowset
flowDensity
4 weeks ago
fredrikwallberg
• 0
0
votes
0
replies
92
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
4 weeks ago
Macsue
• 0
0
votes
1
reply
162
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 4 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
ja569116
• 0
0
votes
2
replies
300
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
5 weeks ago • updated 4 weeks ago
fer_talavera
• 0
0
votes
2
replies
257
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
5 weeks ago • updated 17 days ago
isaac.vock
• 0
0
votes
7
replies
405
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
5 weeks ago • updated 4 weeks ago
needNGS
• 0
0
votes
0
replies
115
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
5 weeks ago
feather-W
• 0
0
votes
0
replies
111
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
5 weeks ago
Ankit
▴ 20
1
vote
5
replies
351
views
fgsea fork
fgsea
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
yimjohns
• 0
395 results • Page
1 of 8
Recent ...
Replies
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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