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r
•
reset
0
votes
0
replies
110
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
8 weeks ago
danalvoronov
▴ 10
0
votes
4
replies
347
views
limma with interaction term
R
biostatistics
limma
Epigenetics
11 weeks ago • updated 8 weeks ago
Jitendra
▴ 10
0
votes
3
replies
476
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
updated 4 months ago by
daenerystargaryen56
• 0 • written 4 months ago by
Sitapriya
• 0
0
votes
0
replies
219
views
multipollutant models
statistics
Regression
r
limma
4 months ago
Jitendra
▴ 10
3
votes
4
replies
520
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
0
votes
10
replies
795
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 8 weeks ago
ScafioRuo
• 0
10
votes
10
replies
6.7k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 5 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
0
votes
2
replies
544
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
8 months ago • updated 7 months ago
yr542
• 0
1
vote
2
replies
593
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
9 months ago
Miguel
• 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
9 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
507
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 10 months ago by
Lluís Revilla Sancho
▴ 730 • written 10 months ago by
Eliza
• 0
0
votes
1
reply
627
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
qiz218591
• 0
0
votes
1
reply
493
views
DEseq2 Single cell data paired design
R
updated 12 months ago by
Marek Gierlinski
▴ 30 • written 12 months ago by
Caro
• 0
0
votes
4
replies
886
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 12 months ago by
swbarnes2
★ 1.3k • written 12 months ago by
Young Tae
• 0
1
vote
3
replies
853
views
tximport error
tximport
r
updated 12 months ago by
Michael Love
41k • written 12 months ago by
Joana
• 0
1
vote
2
replies
877
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
12 months ago
Abdul
▴ 20
0
votes
0
replies
479
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
12 months ago
aymanreffai
• 0
0
votes
4
replies
873
views
Unable to install BiocManager
Biocmanager
R
updated 12 months ago by
L
▴ 50 • written 12 months ago by
sidrah19220
• 0
1
vote
1
reply
1.2k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 12 months ago by
Guido Hooiveld
★ 3.9k • written 12 months ago by
morgan.sobol
• 0
0
votes
13
replies
4.7k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
13 months ago
Laia
▴ 10
1
vote
1
reply
1.2k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5
rhdf
r
updated 13 months ago by
Cynthia
• 0 • written 13 months ago by
Nargil
• 0
0
votes
1
reply
720
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 13 months ago by
Peter Hickey
▴ 740 • written 13 months ago by
cathalgking
▴ 10
0
votes
0
replies
464
views
rDGIdb package: score of the results
rDGIdb
r
13 months ago
HELEN
• 0
2
votes
1
reply
514
views
add column with name in R
name
R
column
updated 13 months ago by
helucro
▴ 70 • written 13 months ago by
sat
• 0
0
votes
4
replies
858
views
how to extract list in quantile in R
R
quantile
list
13 months ago
sat
• 0
0
votes
0
replies
539
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
13 months ago
Manav
• 0
0
votes
0
replies
555
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics
R
Bioconducter
14 months ago
Jitendra
▴ 10
3
votes
2
replies
794
views
how to extract and match information of two filein R
R
column
match
14 months ago
sat
• 0
0
votes
0
replies
502
views
News:
Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics
R
Bioconductor
MassSpectrometry
14 months ago
info
▴ 10
0
votes
17
replies
1.7k
views
How to check linear model
modalmatrix
limma
R
linear
14 months ago
Jitendra
▴ 10
0
votes
3
replies
937
views
batch effect in EPIC array data
statistics
Epigenetics
R
updated 14 months ago by
Lluís Revilla Sancho
▴ 730 • written 14 months ago by
Jitendra
▴ 10
0
votes
1
reply
732
views
customised help function in argparse() in R
command-line
R
command-line-arguments
argparse()
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Learner
• 0
1
vote
2
replies
832
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData
R
microbiomeutilities
Install
14 months ago
abhisek001
• 0
0
votes
3
replies
3.7k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 13 months ago by
Guido Hooiveld
★ 3.9k • written 14 months ago by
YNKIM
• 0
0
votes
4
replies
945
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
14 months ago
Dr.
• 0
0
votes
1
reply
871
views
Extract Intersection Values from Venn
R
Venn
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Dr.
• 0
2
votes
6
replies
1.7k
views
DMRcate
DMRcate
R
DMRcatedata
Markdown
14 months ago
yr542
• 0
0
votes
0
replies
530
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
14 months ago
Luomeng
• 0
2
votes
9
replies
1.2k
views
mas5calls function doesn't work; mirna40cdf problem
R
Bioconductor
mas5calls
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Berna
• 0
0
votes
2
replies
1.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 14 months ago by
Gordon Smyth
50k • written 15 months ago by
Keith
• 0
0
votes
3
replies
917
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures
R
genomation
bed
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
sat
• 0
0
votes
1
reply
640
views
Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression
limma
R
TissueMicroarrayData
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Элина
• 0
4
votes
6
replies
1.2k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
16 months ago
Abdul
▴ 20
0
votes
1
reply
660
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2
MultipleComparison
r
updated 16 months ago by
Michael Love
41k • written 16 months ago by
ncorak
• 0
0
votes
3
replies
1.0k
views
Problem with multiple sequence alignment using AlignSeqs
R
dada2
DECIPHER
updated 16 months ago by
Erik Wright
▴ 150 • written 16 months ago by
Nelli
• 0
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
1
vote
2
replies
783
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
17 months ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
711
views
ape::dnds produces nan value
R
ape
dnds
nan
nanotubes
17 months ago • updated 16 months ago
Working
• 0
2
votes
4
replies
3.4k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
17 months ago
mohammedtoufiq91
▴ 10
1
vote
7
replies
1.4k
views
query regarding error in installation of "goseq" R bioconductor package
R
Bioconductor
Install
updated 17 months ago by
shepherl
3.8k • written 17 months ago by
abhisek001
• 0
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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…
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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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