Showing : r • reset
0
votes
3
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1.6k
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
1
reply
1.1k
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 2.9 years ago by 53k • written 2.9 years ago by • 0
0
votes
2
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1.3k
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 3.0 years ago by • 0 • written 3.0 years ago by ▴ 90
2
votes
4
replies
3.7k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 3.0 years ago by • 0
0
votes
1
reply
1.1k
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
4
votes
6
replies
1.8k
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
3.0 years ago Abdul ▴ 20
3
votes
2
replies
8.9k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 3.0 years ago by ▴ 200 • written 8.0 years ago by • 0
0
votes
3
replies
1.7k
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 3.0 years ago by ▴ 150 • written 3.0 years ago by • 0
4
votes
8
replies
3.5k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.5 years ago by 53k • written 3.0 years ago by ▴ 20
1
vote
2
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1.3k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
3.0 years ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
1.3k
views
ape::dnds produces nan value
R ape dnds nan nanotubes
3.0 years ago Working • 0
0
votes
2
replies
1.6k
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
2
votes
4
replies
5.8k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
1
vote
7
replies
2.4k
views
query regarding error in installation of "goseq" R bioconductor package
R Bioconductor Install
updated 3.0 years ago by 4.2k • written 3.0 years ago by • 0
0
votes
2
replies
1.3k
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
3.0 years ago Sally • 0
1
vote
2
replies
1.5k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
0
votes
4
replies
1.7k
views
paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
3.1 years ago Amit Indap ▴ 10
0
votes
2
replies
1.9k
views
Usinig BiocParallel package in R with M1 MAC
RStudio R M1 BiocParallel Mac
updated 2.9 years ago by • 0 • written 3.1 years ago by • 0
2
votes
3
replies
2.4k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
1
reply
1.4k
views
Biocparallel Error "Error: BiocParallel errors element index: 1, 2, 3 first error: unable to find an inherited method for function ‘bpbackend’ fo…
R OUTRIDER BiocParallel
updated 2.9 years ago by • 0 • written 3.1 years ago by • 0
3
votes
7
replies
2.9k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
2
replies
964
views
How to get accession by the name of species
genbank R accession
3.1 years ago wertykus1 • 0
4
votes
5
replies
2.8k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 2.2 years ago by ▴ 40 • written 3.1 years ago by ▴ 20
0
votes
2
replies
2.4k
views
Cannot install bioconductor DESeq2 package on M1 mac ... any advice?
DESeq2 Install r
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
3
votes
16
replies
3.6k
views
Atena package - error (new user)
RNAseq R Atena
3.1 years ago • updated 2.8 years ago lalanis1 • 0
2
votes
5
replies
4.6k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.1 years ago by 43k • written 4.4 years ago by • 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 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
0
votes
5
replies
3.4k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R ensembldb Annotation
updated 3.1 years ago by ★ 4.1k • written 3.2 years ago by ▴ 30
1
vote
0
replies
900
views
Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
3.2 years ago chen_ying ▴ 10
0
votes
2
replies
1.6k
views
ggplot2 bar plot
R Visualization ggplot2
3.2 years ago Jitendra ▴ 10
0
votes
3
replies
1.8k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.2 years ago Madiha • 0
2
votes
2
replies
4.1k
views
Properly constructing a hypergeometric test
overrepresentation overlap R hypergeometric
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by ▴ 180
0
votes
6
replies
2.9k
views
No differentially expressed genes after DESeq
DESeq2 R
3.2 years ago Zach • 0
5
votes
8
replies
3.0k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
3.2 years ago • updated 3.0 years ago mohammedtoufiq91 ▴ 10
2
votes
4
replies
1.7k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.2 years ago rwan.work • 0
0
votes
2
replies
1.3k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.2 years ago rwan.work • 0
0
votes
1
reply
867
views
Finding negative control in the array using R
R MicroarrayData
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
1
vote
0
replies
1.2k
views
Job: Bioconductor Core developers group opening
R cloud github python git
3.3 years ago Vincent J. Carey, Jr. 6.7k
0
votes
1
reply
2.5k
views
Complex Heatmap - correlation matrix - how to have exact same annotation with same colors for rows and columns?
R heatmaps ComplexHeatmap Heatma
updated 3.3 years ago by ▴ 290 • written 3.3 years ago by • 0
0
votes
0
replies
832
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.3 years ago osieman52 • 0
0
votes
1
reply
1.6k
views
Change my bedgraph file to wig in R
bedgraph R wig
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
votes
1
reply
1.4k
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
4
votes
5
replies
9.0k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.9 years ago by • 0 • written 3.4 years ago by ▴ 50
4
votes
2
replies
1.2k
views
good-first-issue (or similar) GitHub
Culture R GitHub
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
2
replies
1.5k
views
DESeq2 analysis has not been run for this contrast
R DiffBind
3.4 years ago Wang • 0
0
votes
2
replies
1.4k
views
Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression GeneExpression R enrichment DEGseq
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by • 0
1
vote
0
replies
1.0k
views
Mapping patient dataset onto control dataset
Cytometry R Data
3.4 years ago hamiltond ▴ 10
5
votes
8
replies
27k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 16 months ago by ▴ 60 • written 3.4 years ago by ▴ 30
0
votes
4
replies
3.7k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.5 years ago • updated 3.4 years ago Mohamed ▴ 30
2
votes
9
replies
4.1k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.5 years ago Peipei • 0
1,163 results • Page 2 of 24
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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