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48
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
3 days ago
glaciya2018
• 0
0
votes
0
replies
38
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
4 days ago
Sara
• 0
0
votes
0
replies
44
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
4 days ago
Dario Strbenac
★ 1.5k
0
votes
8
replies
276
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 3 days ago by
swbarnes2
★ 1.3k • written 5 days ago by
Aaliya
• 0
0
votes
2
replies
171
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
5 days ago • updated 3 days ago
shuwangxinze1996
• 0
1
vote
13
replies
323
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
7 days ago • updated 3 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
54
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
7 days ago
vaxahey107
• 0
0
votes
0
replies
71
views
I am trying to detect alternative splicing.
ASpli
8 days ago
Sebashish
• 0
0
votes
0
replies
98
views
Warning while loading DEP package
DEP
updated 10 days ago by
shepherl
3.8k • written 10 days ago by
Namrata
• 0
1
vote
2
replies
192
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
10 days ago • updated 9 days ago
Le
• 0
1
vote
2
replies
132
views
Error in champ.load(): The following specified files do not exist
ChAMP
10 days ago
Sherin
• 0
0
votes
1
reply
83
views
Input Question for deseq.r
RSeqAn
updated 10 days ago by
ATpoint
★ 4.0k • written 11 days ago by
Nina
• 0
0
votes
4
replies
204
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
11 days ago • updated 8 days ago
lonn
• 0
0
votes
0
replies
63
views
Enzyme Engineering
BioTIP
11 days ago
bocchemistry
• 0
0
votes
0
replies
80
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
12 days ago • updated 11 days ago
Maliha Tabassum
• 0
0
votes
1
reply
105
views
what is the sampleFiles
chipseq
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
zhulin
• 0
0
votes
0
replies
80
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
12 days ago
Virangika
• 0
0
votes
0
replies
60
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
13 days ago
Henry
▴ 10
0
votes
1
reply
115
views
Deseq2 Rlog transformation
DESeq2
updated 13 days ago by
ATpoint
★ 4.0k • written 14 days ago by
Sahar
• 0
2
votes
2
replies
152
views
[DiffBind] Obtaining normalization factors
DiffBind
16 days ago • updated 12 days ago
Henry
▴ 10
0
votes
3
replies
234
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 10 days ago by
W. Evan Johnson
▴ 850 • written 16 days ago by
schlumbohm
• 0
0
votes
0
replies
79
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
16 days ago
Stevie Pederson
• 0
3
votes
6
replies
242
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
17 days ago
nhaus
▴ 30
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
17 days ago • updated 16 days ago
Shefali
• 0
0
votes
0
replies
117
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
18 days ago
Eryn
• 0
0
votes
0
replies
79
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
18 days ago
Dennis
• 0
0
votes
1
reply
139
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 14 days ago by
Guido Hooiveld
★ 3.9k • written 18 days ago by
Lucie
• 0
0
votes
0
replies
97
views
ggtree tip label position (depth)
ggtree
19 days ago • updated 18 days ago
Roope
• 0
2
votes
6
replies
360
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
20 days ago • updated 19 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
23 days ago
andromeda
• 0
0
votes
1
reply
119
views
Granges regionCounts not returning the expected number of entries
methylKit
23 days ago • updated 22 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
90
views
flowDensity on a flowset
flowDensity
23 days ago
fredrikwallberg
• 0
0
votes
0
replies
80
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
24 days ago
Macsue
• 0
0
votes
1
reply
146
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 26 days ago by
James W. MacDonald
65k • written 27 days ago by
ja569116
• 0
0
votes
2
replies
278
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
27 days ago • updated 23 days ago
fer_talavera
• 0
0
votes
2
replies
241
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
28 days ago • updated 9 days ago
isaac.vock
• 0
0
votes
7
replies
355
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
29 days ago • updated 26 days ago
needNGS
• 0
1
vote
5
replies
314
views
fgsea fork
fgsea
updated 29 days ago by
James W. MacDonald
65k • written 4 weeks ago by
yimjohns
• 0
0
votes
3
replies
317
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
0
votes
1
reply
328
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 18 days ago by
Lluís Revilla Sancho
▴ 730 • written 6 months ago by
karmasstark
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 11 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1
vote
3
replies
825
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 4 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
501
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 19 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
0
votes
1
reply
543
views
CopywriteR output
CopywriteR
updated 23 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
44 results • Page
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Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
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…
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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