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2.5k
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How to interpret MAST coefficients
DifferentialExpression
MAST
updated 8 months ago by
Chenghao
▴ 10 • written 3.3 years ago by
Ismail
• 0
1
vote
2
replies
2.2k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
3.3 years ago
Guandong Shang
▴ 40
0
votes
3
replies
5.8k
views
ASpli: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'sort': 'start' or 'end' canno…
ASpli
updated 2.4 years ago by
andresrabinovich
• 0 • written 3.3 years ago by
thithusuong.nguyen
• 0
0
votes
2
replies
1.4k
views
multiple correction on mean of TPM
TPM
3.3 years ago
Harish.Sudarsanam
• 0
0
votes
1
reply
1.1k
views
Share Annotation Packages
OrgDb
AnnotationDbi
updated 3.3 years ago by
shepherl
4.3k • written 3.3 years ago by
Imad
• 0
0
votes
1
reply
1.4k
views
How to subset a list of genes from a curated reference list of genes
R
subset
DifferentialExpression
updated 3.3 years ago by
Basti
▴ 780 • written 3.3 years ago by
Manav
• 0
0
votes
0
replies
819
views
Problem with ORA in CEMiTool
GeneRegulation
3.3 years ago
j.a.craft
• 0
0
votes
0
replies
757
views
dont find xcmsSet for peak analysis
xcms
3.3 years ago
aline.lafise
• 0
1
vote
0
replies
968
views
Possible to customize the parallel computation used in readGAlignments?
R
readGAlignments
GenomicAlignments
3.3 years ago
chen_ying
▴ 10
0
votes
0
replies
1.3k
views
Gene co-expression network analysis with small sample size
Network
3.3 years ago
Senthil
• 0
0
votes
0
replies
1.2k
views
Edit alignment in msa
alig
msa
Alignment
3.3 years ago
Luis
• 0
0
votes
1
reply
1.2k
views
' Update all/some/none? [a/s/n]: '
forensic
expt
updated 3.3 years ago by
tomhenry099
• 0 • written 3.3 years ago by
attia
• 0
0
votes
3
replies
1.9k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
3.3 years ago
Madiha
• 0
0
votes
1
reply
1.1k
views
I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db
GOfuncR
GO
GOSim
goProfiles
updated 3.3 years ago by
Basti
▴ 780 • written 3.3 years ago by
yeluo
• 0
0
votes
0
replies
718
views
GenVisR - adding on genomic positions to CovGen graph
GenVisR
GenCov
3.3 years ago
Amy_
• 0
0
votes
0
replies
892
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO
GeneOntology
LocusIDtogeneIDconversion
3.3 years ago
BioinFo.X
• 0
0
votes
0
replies
562
views
H bond prediction of two sequences
GeneMeta
generegulation
3.3 years ago
Marcus
• 0
1
vote
0
replies
1.5k
views
adjusted p-values with topGO elim.KS method
topGO
Ontology
DifferentialExpression
3.4 years ago
Kevin Gregory
▴ 10
0
votes
1
reply
2.8k
views
Treeplot by enrichplot
clusterProfiler
enrichplot
treeplot
updated 3.3 years ago by
Guangchuang Yu
★ 1.2k • written 3.4 years ago by
g.neri19
• 0
0
votes
0
replies
985
views
question on the p value for VIPER results by dorothea
RNAseq
VIPER
Doth
3.4 years ago
snowmattin
• 0
0
votes
0
replies
994
views
Outliers
Proteomics
Proteome
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
bansalheena10
• 0
0
votes
0
replies
1.7k
views
HISAT2 and HTSEQ command
HTSeqGenie
3.4 years ago
Maryam.sed1400
• 0
0
votes
0
replies
1.4k
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network
Transcriptomics
MicrobiomeData
RNASEQ
WCGNA
3.4 years ago
Julieta
• 0
2
votes
1
reply
1.3k
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 3.4 years ago by
andres.firrincieli
▴ 50 • written 3.4 years ago by
ikumar2000
▴ 10
0
votes
0
replies
940
views
weighting sample group
monocle
SingleCell
DifferentialExpression
3.4 years ago
Sogand
• 0
0
votes
0
replies
1.5k
views
Simplify - clusterProfiler
RNASeq
simplify
clusterProfiler
enrichGO
simplifyEnrichment
3.4 years ago
estafana.t98
• 0
0
votes
2
replies
1.4k
views
Error message from protein coding prediction with VariantAnnotation
R
VariantAnnotation
3.4 years ago
rwan.work
• 0
1
vote
1
reply
1.3k
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
Mohamed
▴ 30
0
votes
0
replies
631
views
Identification of tissue-specific exons using DEXSeq
#Retina
#RNA-Seq
#DEXSeq
3.4 years ago
osieman52
• 0
0
votes
0
replies
785
views
how to create PHENO_DATA
RNASeq
RNASeqData
RNASeqRData
3.4 years ago
marymshahi2021
• 0
0
votes
2
replies
1.7k
views
Error when using tallyVariants with parallel jobs not returning results
VariantTools
updated 3.4 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.4 years ago by
Imraan
• 0
1
vote
0
replies
912
views
Data format format for summarising each NGS read without collapsing into a count
DataRepresentation
exSTRa
Rsamtools
3.4 years ago
Rick
▴ 10
0
votes
1
reply
2.6k
views
[ NEED HELP >:( ] ggtree Installation Error
ggtree
updated 3.4 years ago by
shepherl
4.3k • written 3.4 years ago by
Muhammad Isa
• 0
1
vote
1
reply
1.7k
views
issue with biomaRt ENSEMBL_MART_SNP
biomaRt
updated 3.4 years ago by
Mike Smith
★ 6.6k • written 3.4 years ago by
Laurel
▴ 10
0
votes
0
replies
772
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.4 years ago
Matthias Munz
▴ 20
0
votes
0
replies
811
views
GO-terms Semantic Similarity Measures: How to decide which method(s) to use?
SemanticSimilarityMeasures
GO-terms
3.4 years ago
Andrew
• 0
0
votes
0
replies
977
views
Finding DEGs between two different datasets using limma
Proteomics
limma
proteomi
3.4 years ago
mfaleevs
• 0
0
votes
2
replies
2.7k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
3.4 years ago
KMS
▴ 20
0
votes
5
replies
3.3k
views
How to add a BioConductor package to a Docker image based on rocker/shiny
docker
3.4 years ago
Sam
▴ 10
1
vote
3
replies
3.2k
views
read.bismark() ->Error in manager$availability[[as.character(result$node)]] <- TRUE : wrong args for environment subassignment
methylSig
bsseq
updated 3.4 years ago by
Peter Hickey
▴ 760 • written 3.4 years ago by
carla.geiger
• 0
0
votes
0
replies
1.2k
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
3.4 years ago
hemangininaik09
• 0
0
votes
0
replies
2.0k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
3.4 years ago
merv
▴ 150
1
vote
4
replies
1.5k
views
Error of PWM not colsum to 1 from package DiffLogo or seqLogo
seqLogo
DiffLogo
3.4 years ago
zhxiaokang
▴ 20
0
votes
1
reply
1.1k
views
getBM Error with certain attribute combinations
biomaRt
ensembldb
updated 3.4 years ago by
ATpoint
★ 5.0k • written 3.4 years ago by
Luisa
• 0
0
votes
0
replies
1.8k
views
Error in GDCDownload and GDCPrepare for TCGA-PAAD Dataset
GDCPrepare
GDCDownload
3.4 years ago
Manav
• 0
0
votes
0
replies
838
views
Tuning the MetaVolcanoR plots
limma
MetaVolcanoR
3.4 years ago
JAcky
• 0
0
votes
0
replies
856
views
maSigPro visualizing individually each plot from each cluster
plot
maSigPro
Clustering
3.4 years ago
oseias.rf.junior
• 0
1
vote
1
reply
1.4k
views
Unable to install "scruff" with BiocManager::install()
scruff
Install
ShortRead
updated 3.4 years ago by
shepherl
4.3k • written 3.4 years ago by
Jackson
• 0
0
votes
2
replies
2.1k
views
long computing time for TSS enrichment score
ATACSeq
updated 2.4 years ago by
Noah
• 0 • written 3.4 years ago by
Taeim
• 0
0
votes
1
reply
1.7k
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 3.4 years ago by
andres.firrincieli
▴ 50 • written 3.4 years ago by
Recep
▴ 20
1,000 results • Page
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Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
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