Showing : R • reset
0
votes
3
replies
1.7k
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
1
reply
1.2k
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 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
2
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1.4k
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 3.2 years ago by • 0 • written 3.3 years ago by ▴ 90
2
votes
4
replies
4.0k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 3.2 years ago by • 0
0
votes
1
reply
1.2k
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
4
votes
6
replies
2.0k
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
3.2 years ago Abdul ▴ 20
3
votes
2
replies
9.4k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 3.2 years ago by ▴ 200 • written 8.2 years ago by • 0
0
votes
3
replies
1.9k
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 3.2 years ago by ▴ 160 • written 3.2 years ago by • 0
4
votes
8
replies
3.6k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.8 years ago by 53k • written 3.2 years ago by ▴ 20
1
vote
2
replies
1.3k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
3.2 years ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
1.3k
views
ape::dnds produces nan value
R ape dnds nan nanotubes
3.2 years ago Working • 0
0
votes
2
replies
1.7k
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 3.2 years ago by ★ 5.0k • written 3.3 years ago by • 0
2
votes
4
replies
6.3k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.2 years ago mohammedtoufiq91 ▴ 10
1
vote
7
replies
2.6k
views
query regarding error in installation of "goseq" R bioconductor package
R Bioconductor Install
updated 3.2 years ago by 4.3k • written 3.2 years ago by • 0
0
votes
2
replies
1.4k
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
3.3 years ago Sally • 0
1
vote
2
replies
1.6k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.3 years ago mohammedtoufiq91 ▴ 10
0
votes
4
replies
1.8k
views
paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
3.3 years ago Amit Indap ▴ 10
0
votes
2
replies
2.1k
views
Usinig BiocParallel package in R with M1 MAC
RStudio R M1 BiocParallel Mac
updated 3.1 years ago by • 0 • written 3.3 years ago by • 0
2
votes
3
replies
2.6k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
votes
1
reply
1.5k
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 3.1 years ago by • 0 • written 3.3 years ago by • 0
3
votes
7
replies
3.0k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
votes
2
replies
990
views
How to get accession by the name of species
genbank R accession
3.3 years ago wertykus1 • 0
4
votes
5
replies
2.9k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 2.4 years ago by ▴ 40 • written 3.4 years ago by ▴ 20
0
votes
2
replies
2.5k
views
Cannot install bioconductor DESeq2 package on M1 mac ... any advice?
DESeq2 Install r
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
3
votes
16
replies
3.7k
views
Atena package - error (new user)
RNAseq R Atena
3.4 years ago • updated 3.1 years ago lalanis1 • 0
2
votes
5
replies
4.8k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.3 years ago by 43k • written 4.7 years ago by • 0
0
votes
1
reply
1.5k
views
How to subset a list of genes from a curated reference list of genes
R subset DifferentialExpression
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
0
votes
5
replies
3.8k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R ensembldb Annotation
updated 3.4 years ago by ★ 4.1k • written 3.4 years ago by ▴ 30
1
vote
0
replies
987
views
Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
3.4 years ago chen_ying ▴ 10
0
votes
2
replies
1.7k
views
ggplot2 bar plot
R Visualization ggplot2
3.4 years ago Jitendra ▴ 10
0
votes
3
replies
2.0k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.4 years ago Madiha • 0
2
votes
2
replies
4.9k
views
Properly constructing a hypergeometric test
overrepresentation overlap R hypergeometric
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by ▴ 180
0
votes
6
replies
3.1k
views
No differentially expressed genes after DESeq
DESeq2 R
3.4 years ago Zach • 0
5
votes
8
replies
3.2k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
3.4 years ago • updated 3.2 years ago mohammedtoufiq91 ▴ 10
2
votes
4
replies
1.8k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.4 years ago rwan.work • 0
0
votes
2
replies
1.4k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.5 years ago rwan.work • 0
0
votes
1
reply
928
views
Finding negative control in the array using R
R MicroarrayData
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
1
vote
0
replies
1.2k
views
Job: Bioconductor Core developers group opening
R cloud github python git
3.5 years ago Vincent J. Carey, Jr. 6.7k
0
votes
1
reply
2.7k
views
Complex Heatmap - correlation matrix - how to have exact same annotation with same colors for rows and columns?
R heatmaps ComplexHeatmap Heatma
updated 3.5 years ago by ▴ 290 • written 3.5 years ago by • 0
0
votes
0
replies
882
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.5 years ago osieman52 • 0
0
votes
1
reply
1.7k
views
Change my bedgraph file to wig in R
bedgraph R wig
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
votes
1
reply
1.5k
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
4
votes
5
replies
9.3k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 3.1 years ago by • 0 • written 3.6 years ago by ▴ 50
4
votes
2
replies
1.3k
views
good-first-issue (or similar) GitHub
Culture R GitHub
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
2
replies
1.5k
views
DESeq2 analysis has not been run for this contrast
R DiffBind
3.6 years ago Wang • 0
0
votes
2
replies
1.5k
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 3.6 years ago by ★ 1.4k • written 3.6 years ago by • 0
1
vote
0
replies
1.0k
views
Mapping patient dataset onto control dataset
Cytometry R Data
3.6 years ago hamiltond ▴ 10
6
votes
8
replies
30k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 18 months ago by ▴ 60 • written 3.7 years ago by ▴ 30
0
votes
4
replies
4.0k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.7 years ago Mohamed ▴ 30
2
votes
9
replies
4.6k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.7 years ago Peipei • 0
1,163 results • Page 2 of 24
Recent ...
Replies
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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