Showing : r • reset
0
votes
2
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195
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
6 weeks ago • updated 18 days ago yr542 • 0
1
vote
2
replies
203
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
8 weeks ago Miguel • 0
2
votes
5
replies
485
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 weeks ago • updated 8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
267
views
Gene enrichment analysis
analysis R GOfuncR
updated 3 months ago by ▴ 720 • written 3 months ago by • 0
0
votes
2
replies
860
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 3 months ago by • 0 • written 2.6 years ago by • 0
0
votes
1
reply
335
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 4 months ago by 48k • written 4 months ago by • 0
0
votes
1
reply
270
views
DEseq2 Single cell data paired design
R
updated 5 months ago by ▴ 10 • written 5 months ago by • 0
0
votes
4
replies
389
views
Combine RNA-seq
BatchEffect R rnaseq
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
1
vote
3
replies
406
views
tximport error
tximport r
updated 5 months ago by 40k • written 5 months ago by • 0
1
vote
2
replies
484
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
5 months ago Abdul ▴ 20
0
votes
0
replies
217
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
5 months ago aymanreffai • 0
1
vote
1
reply
476
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 5 months ago by ★ 3.7k • written 5 months ago by • 0
0
votes
4
replies
442
views
Unable to install BiocManager
Biocmanager R
updated 5 months ago by ▴ 50 • written 5 months ago by • 0
1
vote
1
reply
622
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 6 months ago by • 0 • written 6 months ago by • 0
0
votes
13
replies
1.6k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
6 months ago Laia ▴ 10
0
votes
3
replies
1.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 6 months ago by ★ 3.7k • written 7 months ago by • 0
0
votes
1
reply
322
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 6 months ago by ▴ 650 • written 6 months ago by ▴ 10
0
votes
0
replies
247
views
rDGIdb package: score of the results
rDGIdb r
6 months ago HELEN • 0
2
votes
1
reply
294
views
add column with name in R
name R column
updated 6 months ago by ▴ 70 • written 6 months ago by • 0
0
votes
4
replies
429
views
how to extract list in quantile in R
R quantile list
6 months ago sat • 0
0
votes
0
replies
274
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
6 months ago Manav • 0
0
votes
0
replies
264
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
6 months ago Jitendra ▴ 10
3
votes
2
replies
373
views
how to extract and match information of two filein R
R column match
6 months ago sat • 0
0
votes
0
replies
244
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
7 months ago info ▴ 10
0
votes
17
replies
994
views
How to check linear model
modalmatrix limma R linear
7 months ago • updated 6 months ago Jitendra ▴ 10
0
votes
1
reply
372
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 7 months ago by 63k • written 7 months ago by • 0
0
votes
3
replies
525
views
batch effect in EPIC array data
statistics Epigenetics R
updated 7 months ago by ▴ 720 • written 7 months ago by ▴ 10
1
vote
2
replies
454
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
7 months ago abhisek001 • 0
0
votes
4
replies
525
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
7 months ago Dr. • 0
0
votes
1
reply
408
views
Extract Intersection Values from Venn
R Venn
updated 7 months ago by 63k • written 7 months ago by • 0
2
votes
6
replies
844
views
DMRcate
DMRcate R DMRcatedata Markdown
7 months ago yr542 • 0
0
votes
0
replies
280
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
7 months ago Luomeng • 0
2
votes
9
replies
805
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 7 months ago by 63k • written 7 months ago by • 0
0
votes
2
replies
709
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 7 months ago by 48k • written 8 months ago by • 0
0
votes
3
replies
503
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 8 months ago by 63k • written 8 months ago by • 0
0
votes
1
reply
367
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 8 months ago by 48k • written 8 months ago by • 0
0
votes
2
replies
507
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 9 months ago by • 0 • written 10 months ago by ▴ 70
2
votes
4
replies
1.2k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 10 months ago by • 0
0
votes
1
reply
446
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 9 months ago by 40k • written 9 months ago by • 0
4
votes
6
replies
729
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
9 months ago Abdul ▴ 20
1
vote
2
replies
5.1k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 9 months ago by ▴ 20 • written 5.8 years ago by • 0
0
votes
3
replies
656
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 9 months ago by ▴ 150 • written 9 months ago by • 0
4
votes
8
replies
1.3k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 4 months ago by 48k • written 9 months ago by ▴ 20
1
vote
2
replies
513
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
9 months ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
451
views
ape::dnds produces nan value
R ape dnds nan nanotubes
9 months ago Working • 0
0
votes
2
replies
633
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 9 months ago by ★ 3.4k • written 10 months ago by • 0
2
votes
4
replies
2.0k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
9 months ago mohammedtoufiq91 ▴ 10
1
vote
7
replies
833
views
query regarding error in installation of "goseq" R bioconductor package
R Bioconductor Install
updated 10 months ago by 3.5k • written 10 months ago by • 0
0
votes
2
replies
450
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization R cqn
10 months ago Sally • 0
1
vote
2
replies
518
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
10 months ago mohammedtoufiq91 ▴ 10
50 results • Page 1 of 1
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Comment: Problems with FLOWAI by SHASHI • 0
please try this using short path name and keeping your fcs file and wsp file in your local directory https://youtu.be/xLeqE7PNYzA
Comment: DataFrame Construction With Non-standard Column by Hervé Pagès 16k
SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…
Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu by swbarnes2 ★ 1.3k
The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…
Answer: Remove duplicates of colData in TreeSummarizedExperiment by Michael Love 40k
Copying my code from Slack for posterity. James' code is more streamlined for this step I think. ``` # make a dataset that has duplicate s…
Comment: DataFrame Construction With Non-standard Column by James W. MacDonald 63k
Oh, ok. I understand. Technically both should work according to what the help page for `DataFrame` says (both `SimpleList` and `list` have …
Votes
A: LIMMA dupcor() function time issue.
A: LIMMA dupcor() function time issue.
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
Answer: DataFrame Construction With Non-standard Column
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