3
votes
18
replies
2.8k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 7 days ago shepherl 3.8k
7
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28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 11 weeks ago by 50k • written 9.1 years ago by ★ 7.9k
0
votes
7
replies
610
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
7 weeks ago • updated 1 day ago shepherl 3.8k
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 4 months ago by • 0 • written 11.3 years ago by ▴ 280
1
vote
8
replies
1.5k
views
News: Final List of Deprecated Package Bioc 3.9
deprecation release software experimentData News
written 5.1 years ago by 3.8k
2
votes
6
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2.5k
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Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 6 weeks ago by • 0 • written 6.3 years ago by ▴ 10
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 4 weeks ago by • 0 • written 8.9 years ago by ▴ 150
0
votes
5
replies
1.1k
views
pathway finding software
written 15.5 years ago by ▴ 250
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 22 days ago by 50k • written 9.8 years ago by ▴ 40
13
votes
22
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26k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 8 weeks ago by 41k • written 7.8 years ago by ▴ 30
2
votes
11
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1.5k
views
Not able to download recount3 data
recount3
updated 11 months ago by ★ 1.0k • written 16 months ago by ▴ 20
0
votes
5
replies
5.7k
views
masigpro Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument
masigpro
updated 8 months ago by • 0 • written 8.9 years ago by ▴ 120
0
votes
7
replies
406
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago fr8712ca-s • 0
3
votes
5
replies
1.6k
views
Error: 'IdClusters'
DECIPHER
updated 11 months ago by ▴ 10 • written 14 months ago by • 0
1
vote
6
replies
2.6k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.4 years ago by ▴ 10
2
votes
9
replies
1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 5 months ago by ▴ 50 • written 6 months ago by ▴ 30
1
vote
3
replies
3.0k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 5 weeks ago by ▴ 20 • written 6.5 years ago by ▴ 100
0
votes
11
replies
3.7k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 12 weeks ago by ▴ 170 • written 7.1 years ago by ★ 2.0k
0
votes
5
replies
2.0k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 10.3 years ago by ★ 13k
9
votes
11
replies
5.7k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 6 weeks ago by 3.8k • written 2.2 years ago by ▴ 40
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
4
votes
10
replies
1.7k
views
Archives prior to 3.15 gone
archive bioconductor
updated 6 months ago by 3.8k • written 19 months ago by ▴ 30
1
vote
10
replies
2.0k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 17 months ago by • 0
0
votes
4
replies
732
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
0
votes
3
replies
1.6k
views
extract rsids of SNPs using their genomic positions
rsids SNPlocs.Hsapiens.dbSNP150.GRCh38
written 9 months ago by • 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
0
votes
6
replies
1.2k
views
LIMMA : design (1, 2, 3, 3 ) , I got EXCITING results, what could be the logic, since i have 2 replicates for 3rd group only ?
affy affy
updated 7 weeks ago by 50k • written 19.0 years ago by ★ 1.1k
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by 50k • written 12.0 years ago by ▴ 180
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by ▴ 180 • written 16 months ago by ▴ 30
7
votes
18
replies
2.9k
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Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 3 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
2
votes
3
replies
1.1k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 3 months ago by • 0 • written 2.8 years ago by ▴ 470
2
votes
8
replies
486
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 28 days ago by 50k • written 29 days ago by • 0
6
votes
5
replies
1.1k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 7 months ago by ▴ 740 • written 8 months ago by ▴ 20
0
votes
6
replies
1.5k
views
mailman bugs
Website
21.2 years ago • updated 10 months ago Gordon Smyth 50k
2
votes
3
replies
794
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 8 months ago by • 0 • written 8.4 years ago by ▴ 60
1
vote
4
replies
6.1k
views
Error loading impute(): '/usr/lib/libgfortran.5.dylib' (no such file)
Install impute
updated 11 months ago by • 0 • written 2.2 years ago by • 0
1
vote
9
replies
5.2k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.1 years ago by • 0
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
0
votes
6
replies
1.4k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 12 months ago by • 0 • written 2.7 years ago by • 0
2
votes
6
replies
1.3k
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 11 months ago by ★ 1.0k • written 16 months ago by • 0
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 5 months ago by 50k • written 12.4 years ago by ★ 13k
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 20 days ago by • 0 • written 5.4 years ago by ★ 3.9k
1
vote
5
replies
1.6k
views
rowsum or similar for RleArray?
delayedarray rowsum
written 6.6 years ago by ▴ 170
0
votes
7
replies
1.5k
views
Unable to install RefPlus - R=4.3.1, BiocManager=3.18
Install instal
updated 5 months ago by 65k • written 5 months ago by • 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
1
vote
13
replies
11k
views
unable to access index for repository
Bioconductor ConsensusClusterPlus
updated 8 months ago by • 0 • written 16 months ago by • 0
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.8 years ago by • 0
2
votes
3
replies
1.5k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 6 weeks ago by • 0 • written 17 months ago by • 0
1,749 results • Page 1 of 35
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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