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0
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15
views
Dominance Index for Shotgun Metagenomics Data
microbiome
6 hours ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
34
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
1 day ago
glaciya2018
• 0
0
votes
0
replies
24
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
2 days ago
Sara
• 0
0
votes
0
replies
33
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
2 days ago
Dario Strbenac
★ 1.5k
0
votes
8
replies
240
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 1 day ago by
swbarnes2
★ 1.3k • written 3 days ago by
Aaliya
• 0
0
votes
2
replies
130
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
3 days ago • updated 1 day ago
shuwangxinze1996
• 0
1
vote
13
replies
278
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
5 days ago • updated 1 day ago
fernanda.backsouza
▴ 10
0
votes
0
replies
44
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
5 days ago
vaxahey107
• 0
0
votes
0
replies
63
views
I am trying to detect alternative splicing.
ASpli
6 days ago
Sebashish
• 0
0
votes
0
replies
88
views
Warning while loading DEP package
DEP
updated 8 days ago by
shepherl
3.8k • written 8 days ago by
Namrata
• 0
1
vote
2
replies
183
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
8 days ago • updated 7 days ago
Le
• 0
1
vote
2
replies
126
views
Error in champ.load(): The following specified files do not exist
ChAMP
8 days ago
Sherin
• 0
0
votes
1
reply
80
views
Input Question for deseq.r
RSeqAn
updated 8 days ago by
ATpoint
★ 4.0k • written 8 days ago by
Nina
• 0
0
votes
4
replies
199
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
9 days ago • updated 6 days ago
lonn
• 0
0
votes
0
replies
58
views
Enzyme Engineering
BioTIP
9 days ago
bocchemistry
• 0
0
votes
0
replies
80
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
9 days ago
Maliha Tabassum
• 0
0
votes
1
reply
101
views
what is the sampleFiles
chipseq
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
zhulin
• 0
0
votes
0
replies
76
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
10 days ago
Virangika
• 0
0
votes
0
replies
58
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
11 days ago
Henry
▴ 10
0
votes
1
reply
112
views
Deseq2 Rlog transformation
DESeq2
updated 11 days ago by
ATpoint
★ 4.0k • written 12 days ago by
Sahar
• 0
2
votes
2
replies
150
views
[DiffBind] Obtaining normalization factors
DiffBind
14 days ago • updated 10 days ago
Henry
▴ 10
0
votes
3
replies
227
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 8 days ago by
W. Evan Johnson
▴ 850 • written 14 days ago by
schlumbohm
• 0
0
votes
0
replies
76
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
14 days ago
Stevie Pederson
• 0
3
votes
6
replies
237
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
15 days ago
nhaus
▴ 30
0
votes
1
reply
159
views
DESeq2 gives an error and R crashes
DESeq2
15 days ago • updated 14 days ago
Shefali
• 0
0
votes
0
replies
115
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
15 days ago
Eryn
• 0
0
votes
0
replies
79
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
15 days ago
Dennis
• 0
0
votes
1
reply
137
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 12 days ago by
Guido Hooiveld
★ 3.9k • written 15 days ago by
Lucie
• 0
0
votes
0
replies
96
views
ggtree tip label position (depth)
ggtree
17 days ago • updated 16 days ago
Roope
• 0
2
votes
6
replies
354
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
18 days ago • updated 17 days ago
Chris
• 0
0
votes
0
replies
134
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
21 days ago
andromeda
• 0
0
votes
1
reply
118
views
Granges regionCounts not returning the expected number of entries
methylKit
21 days ago • updated 20 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
88
views
flowDensity on a flowset
flowDensity
21 days ago
fredrikwallberg
• 0
0
votes
0
replies
79
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
22 days ago
Macsue
• 0
0
votes
1
reply
144
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 24 days ago by
James W. MacDonald
65k • written 25 days ago by
ja569116
• 0
0
votes
2
replies
276
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
25 days ago • updated 21 days ago
fer_talavera
• 0
0
votes
2
replies
238
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
25 days ago • updated 7 days ago
isaac.vock
• 0
0
votes
7
replies
351
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
27 days ago • updated 24 days ago
needNGS
• 0
0
votes
0
replies
99
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
28 days ago
feather-W
• 0
0
votes
0
replies
97
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
28 days ago
Ankit
▴ 20
1
vote
5
replies
301
views
fgsea fork
fgsea
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
yimjohns
• 0
0
votes
0
replies
84
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
29 days ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
108
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
4 weeks ago
gshweta95
• 0
3
votes
3
replies
369
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 4 weeks ago by
alan.ocallaghan
▴ 160 • written 4 weeks ago by
Najla Abassi
• 0
2
votes
1
reply
192
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 4 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
enee
▴ 10
0
votes
0
replies
109
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
5 weeks ago
nromerov
• 0
1
vote
3
replies
245
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 5 weeks ago by
Marcel Ramos
690 • written 5 weeks ago by
Astrid Deschênes
• 0
0
votes
0
replies
118
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
5 weeks ago
mayra.haedo
• 0
0
votes
0
replies
106
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
5 weeks ago
taylor.witte
• 0
0
votes
0
replies
126
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
5 weeks ago
erbrocato
• 0
1,000 results • Page
1 of 20
Recent ...
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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