0
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0
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38
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
2 days ago glaciya2018 • 0
0
votes
0
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29
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Differential splicing from SGSeq analysis
DEXSeq SGSeq
2 days ago Sara • 0
0
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0
replies
36
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
2 days ago Dario Strbenac ★ 1.5k
0
votes
8
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256
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 2 days ago by ★ 1.3k • written 3 days ago by • 0
0
votes
2
replies
152
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
4 days ago • updated 2 days ago shuwangxinze1996 • 0
1
vote
13
replies
298
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
5 days ago • updated 2 days ago fernanda.backsouza ▴ 10
0
votes
0
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45
views
Unlocking Potential: NURS FPX Strategies and Insights
levi NURSFPX ragene20sttranscriptcluster.db ssrch
6 days ago vaxahey107 • 0
0
votes
0
replies
64
views
I am trying to detect alternative splicing.
ASpli
6 days ago Sebashish • 0
0
votes
0
replies
91
views
Warning while loading DEP package
DEP
updated 8 days ago by 3.8k • written 8 days ago by • 0
1
vote
2
replies
191
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
9 days ago • updated 8 days ago Le • 0
1
vote
2
replies
129
views
Error in champ.load(): The following specified files do not exist
ChAMP
9 days ago • updated 8 days ago Sherin • 0
0
votes
1
reply
82
views
Input Question for deseq.r
RSeqAn
updated 9 days ago by ★ 4.0k • written 9 days ago by • 0
0
votes
4
replies
201
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 days ago • updated 7 days ago lonn • 0
0
votes
0
replies
60
views
Enzyme Engineering
BioTIP
10 days ago bocchemistry • 0
0
votes
0
replies
80
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror IsoCorrectoR
10 days ago Maliha Tabassum • 0
0
votes
1
reply
103
views
what is the sampleFiles
chipseq
updated 10 days ago by 65k • written 11 days ago by • 0
0
votes
0
replies
78
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
11 days ago Virangika • 0
0
votes
0
replies
59
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
11 days ago Henry ▴ 10
0
votes
1
reply
114
views
Deseq2 Rlog transformation
DESeq2
updated 12 days ago by ★ 4.0k • written 13 days ago by • 0
2
votes
2
replies
151
views
[DiffBind] Obtaining normalization factors
DiffBind
14 days ago • updated 11 days ago Henry ▴ 10
0
votes
3
replies
232
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A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 8 days ago by ▴ 850 • written 15 days ago by • 0
0
votes
0
replies
77
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
15 days ago Stevie Pederson • 0
3
votes
6
replies
238
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
16 days ago • updated 15 days ago nhaus ▴ 30
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
16 days ago • updated 15 days ago Shefali • 0
0
votes
0
replies
116
views
LearnTaxa with custom Silva
DECIPHER LearnTaxa
16 days ago Eryn • 0
0
votes
0
replies
79
views
queryDGIdb lexical error for some genes
lexicalerror rDGIdb DGIdb json
16 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 ★ 3.9k • written 16 days ago by • 0
0
votes
0
replies
97
views
ggtree tip label position (depth)
ggtree
18 days ago • updated 17 days ago Roope • 0
2
votes
6
replies
355
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
18 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
22 days ago • updated 21 days ago Modoc Kesner ▴ 10
0
votes
0
replies
88
views
flowDensity on a flowset
flowDensity
22 days ago fredrikwallberg • 0
0
votes
0
replies
80
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
23 days ago Macsue • 0
0
votes
1
reply
145
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 24 days ago by 65k • written 26 days ago by • 0
0
votes
2
replies
277
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR CopyhelpeR
26 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
26 days ago • updated 7 days ago isaac.vock • 0
0
votes
7
replies
353
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
29 days ago feather-W • 0
0
votes
0
replies
100
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
29 days ago Ankit ▴ 20
1
vote
5
replies
306
views
fgsea fork
fgsea
updated 28 days ago by 65k • written 29 days ago by • 0
0
votes
0
replies
86
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
4 weeks ago Pierre Lindenbaum ▴ 10
3
votes
3
replies
372
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 4 weeks ago by ▴ 160 • written 4 weeks ago by • 0
0
votes
0
replies
109
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
4 weeks ago gshweta95 • 0
2
votes
1
reply
196
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 4 weeks ago by ★ 3.9k • written 5 weeks ago by ▴ 10
0
votes
0
replies
110
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
5 weeks ago nromerov • 0
1
vote
3
replies
249
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 5 weeks ago by 690 • written 5 weeks ago by • 0
0
votes
0
replies
119
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray cdf crlmm
5 weeks ago mayra.haedo • 0
0
votes
0
replies
108
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry flowWorkspace flowCore
5 weeks ago taylor.witte • 0
0
votes
0
replies
127
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
5 weeks ago erbrocato • 0
1
vote
4
replies
275
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
5 weeks ago samuel.channon • 0
1,000 results • Page 1 of 20
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
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…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
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)
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