Showing : R • reset
0
votes
3
replies
1.6k
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
votes
1
reply
1.0k
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 2.8 years ago by 53k • written 2.8 years ago by • 0
0
votes
2
replies
1.2k
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 2.8 years ago by • 0 • written 2.9 years ago by ▴ 90
2
votes
4
replies
3.5k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 2.9 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 2.8 years ago by 43k • written 2.8 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
2.8 years ago Abdul ▴ 20
3
votes
2
replies
8.7k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 2.8 years ago by ▴ 200 • written 7.8 years ago by • 0
0
votes
3
replies
1.6k
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 2.8 years ago by ▴ 150 • written 2.9 years ago by • 0
4
votes
8
replies
3.4k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.4 years ago by 53k • written 2.9 years ago by ▴ 20
1
vote
2
replies
1.2k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
2.9 years ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
1.1k
views
ape::dnds produces nan value
R ape dnds nan nanotubes
2.9 years ago Working • 0
0
votes
2
replies
1.5k
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
2
votes
4
replies
5.7k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
2.9 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 2.9 years ago by 4.2k • written 2.9 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
2.9 years ago Sally • 0
1
vote
2
replies
1.4k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
2.9 years ago mohammedtoufiq91 ▴ 10
0
votes
4
replies
1.6k
views
paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
2.9 years ago Amit Indap ▴ 10
0
votes
2
replies
1.8k
views
Usinig BiocParallel package in R with M1 MAC
RStudio R M1 BiocParallel Mac
updated 2.8 years ago by • 0 • written 2.9 years ago by • 0
2
votes
3
replies
2.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.9 years ago by 53k • written 2.9 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 2.8 years ago by • 0 • written 2.9 years ago by • 0
3
votes
7
replies
2.8k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 2.9 years ago by 53k • written 3.0 years ago by • 0
0
votes
2
replies
917
views
How to get accession by the name of species
genbank R accession
2.9 years ago wertykus1 • 0
4
votes
5
replies
2.7k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 2.0 years ago by ▴ 40 • written 3.0 years ago by ▴ 20
0
votes
2
replies
2.3k
views
Cannot install bioconductor DESeq2 package on M1 mac ... any advice?
DESeq2 Install r
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
3
votes
16
replies
3.5k
views
Atena package - error (new user)
RNAseq R Atena
3.0 years ago • updated 2.7 years ago lalanis1 • 0
2
votes
5
replies
4.5k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.0 years ago by 43k • written 4.3 years ago by • 0
0
votes
1
reply
1.3k
views
How to subset a list of genes from a curated reference list of genes
R subset DifferentialExpression
updated 3.0 years ago by ▴ 780 • written 3.0 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 3.0 years ago by ★ 4.1k • written 3.0 years ago by ▴ 30
1
vote
0
replies
841
views
Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
3.0 years ago chen_ying ▴ 10
0
votes
2
replies
1.4k
views
ggplot2 bar plot
R Visualization ggplot2
3.0 years ago Jitendra ▴ 10
0
votes
3
replies
1.7k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.0 years ago Madiha • 0
2
votes
2
replies
4.1k
views
Properly constructing a hypergeometric test
overrepresentation overlap R hypergeometric
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 180
0
votes
6
replies
2.9k
views
No differentially expressed genes after DESeq
DESeq2 R
3.0 years ago Zach • 0
5
votes
8
replies
2.9k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
3.1 years ago • updated 2.9 years ago mohammedtoufiq91 ▴ 10
2
votes
4
replies
1.6k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.1 years ago rwan.work • 0
0
votes
2
replies
1.3k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.1 years ago rwan.work • 0
0
votes
1
reply
820
views
Finding negative control in the array using R
R MicroarrayData
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
vote
0
replies
1.1k
views
Job: Bioconductor Core developers group opening
R cloud github python git
3.1 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 3.1 years ago by ▴ 290 • written 3.1 years ago by • 0
0
votes
0
replies
794
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.2 years ago osieman52 • 0
0
votes
1
reply
1.6k
views
Change my bedgraph file to wig in R
bedgraph R wig
updated 3.2 years ago by ★ 5.0k • written 3.2 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 3.2 years ago by 53k • written 3.2 years ago by • 0
4
votes
5
replies
8.8k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.8 years ago by • 0 • written 3.2 years ago by ▴ 50
4
votes
2
replies
1.1k
views
good-first-issue (or similar) GitHub
Culture R GitHub
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
2
replies
1.5k
views
DESeq2 analysis has not been run for this contrast
R DiffBind
3.2 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 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
1
vote
0
replies
854
views
Mapping patient dataset onto control dataset
Cytometry R Data
3.3 years ago hamiltond ▴ 10
5
votes
8
replies
27k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 14 months ago by ▴ 60 • written 3.3 years ago by ▴ 30
0
votes
4
replies
3.5k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.3 years ago Mohamed ▴ 30
2
votes
9
replies
4.0k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.3 years ago Peipei • 0
1,163 results • Page 2 of 24
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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