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0
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replies
38
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
2 days ago
glaciya2018
• 0
0
votes
2
replies
155
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
0
votes
8
replies
258
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 2 days ago by
swbarnes2
★ 1.3k • written 4 days ago by
Aaliya
• 0
1
vote
13
replies
304
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
6 days ago • updated 2 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
29
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
3 days ago
Sara
• 0
0
votes
0
replies
37
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
3 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
821
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 3 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
0
replies
46
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
7 days ago
Sebashish
• 0
0
votes
4
replies
201
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
10 days ago • updated 7 days ago
lonn
• 0
0
votes
2
replies
238
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
26 days ago • updated 8 days ago
isaac.vock
• 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
0
votes
3
replies
232
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 9 days ago by
W. Evan Johnson
▴ 850 • written 15 days ago by
schlumbohm
• 0
0
votes
0
replies
91
views
Warning while loading DEP package
DEP
updated 9 days ago by
shepherl
3.8k • written 9 days ago by
Namrata
• 0
1
vote
2
replies
129
views
Error in champ.load(): The following specified files do not exist
ChAMP
9 days ago
Sherin
• 0
0
votes
1
reply
83
views
Input Question for deseq.r
RSeqAn
updated 9 days ago by
ATpoint
★ 4.0k • written 9 days ago by
Nina
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 10 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 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 11 days ago by
James W. MacDonald
65k • written 11 days ago by
zhulin
• 0
2
votes
2
replies
151
views
[DiffBind] Obtaining normalization factors
DiffBind
15 days ago • updated 11 days ago
Henry
▴ 10
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
12 days ago
Henry
▴ 10
0
votes
1
reply
115
views
Deseq2 Rlog transformation
DESeq2
updated 12 days ago by
ATpoint
★ 4.0k • written 13 days ago by
Sahar
• 0
0
votes
1
reply
138
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 13 days ago by
Guido Hooiveld
★ 3.9k • written 16 days ago by
Lucie
• 0
0
votes
0
replies
77
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
15 days ago
Stevie Pederson
• 0
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
16 days ago • updated 15 days ago
Shefali
• 0
3
votes
6
replies
238
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
16 days ago
nhaus
▴ 30
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
328
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 17 days ago by
Lluís Revilla Sancho
▴ 730 • written 6 months ago by
karmasstark
• 0
0
votes
0
replies
97
views
ggtree tip label position (depth)
ggtree
18 days ago • updated 17 days ago
Roope
• 0
0
votes
1
reply
499
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 18 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
2
votes
6
replies
358
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
19 days ago • updated 18 days ago
Chris
• 0
0
votes
1
reply
119
views
Granges regionCounts not returning the expected number of entries
methylKit
22 days ago • updated 21 days ago
Modoc Kesner
▴ 10
0
votes
1
reply
540
views
CopywriteR output
CopywriteR
updated 21 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 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
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
22 days ago • updated 21 days ago
andromeda
• 0
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 25 days ago by
James W. MacDonald
65k • written 26 days ago by
ja569116
• 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
28 days ago • updated 25 days ago
needNGS
• 0
0
votes
3
replies
316
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
1
vote
5
replies
308
views
fgsea fork
fgsea
updated 28 days ago by
James W. MacDonald
65k • written 29 days ago by
yimjohns
• 0
0
votes
0
replies
100
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
46 results • Page
1 of 1
Recent ...
Replies
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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