3
votes
18
replies
3.0k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 4 weeks ago shepherl 3.9k
7
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28
replies
6.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 3 months ago by 50k • written 9.2 years ago by ★ 7.9k
0
votes
7
replies
746
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
11 weeks ago • updated 24 days ago shepherl 3.9k
0
votes
21
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6.6k
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BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 5 months ago by • 0 • written 11.4 years ago by ▴ 280
2
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6
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2.6k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 10 weeks ago by • 0 • written 6.3 years ago by ▴ 10
0
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6
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3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
13
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22
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27k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 12 weeks ago by 42k • written 7.9 years ago by ▴ 30
4
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16
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7.4k
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Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 8 weeks ago by • 0 • written 9.0 years ago by ▴ 150
3
votes
5
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1.7k
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Error: 'IdClusters'
DECIPHER
updated 11 months ago by ▴ 10 • written 15 months ago by • 0
2
votes
9
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1.2k
views
object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 6 months ago by ▴ 50 • written 6 months ago by ▴ 30
1
vote
6
replies
2.7k
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 7.5 years ago by ▴ 10
0
votes
7
replies
458
views
DESeq2 filtering vs edgeR filtering
DESeq2
9 weeks ago • updated 7 weeks ago fr8712ca-s • 0
0
votes
5
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5.8k
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masigpro Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument
masigpro
updated 9 months ago by • 0 • written 9.0 years ago by ▴ 120
0
votes
5
replies
1.2k
views
pathway finding software
written 15.5 years ago by ▴ 250
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 8 weeks ago by ▴ 20 • written 6.6 years ago by ▴ 100
0
votes
11
replies
3.8k
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bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 3 months ago by ▴ 180 • written 7.1 years ago by ★ 2.0k
0
votes
5
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2.0k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 10.4 years ago by ★ 13k
0
votes
11
replies
1.3k
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Unable to install DESeq2
DESeq2
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
9
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5.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.2 years ago by • 0
1
vote
16
replies
3.4k
views
error in ChAMP loading file
ChAMP
updated 9 weeks ago by • 0 • written 18 months ago by • 0
1
vote
10
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2.1k
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Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 18 months ago by • 0
0
votes
11
replies
2.1k
views
globaltest question
Pathways probe affy Pathways probe affy
written 17.7 years ago by ▴ 30
2
votes
3
replies
1.7k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 8 months ago by 50k • written 8 months ago by • 0
2
votes
3
replies
706
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Rsubread: subjunc() loads index repeatedly
Rsubread
10 months ago • updated 9 months ago Gerhard Thallinger ▴ 180
5
votes
8
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3.9k
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Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
0
votes
6
replies
1.5k
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mailman bugs
Website
21.3 years ago • updated 11 months ago Gordon Smyth 50k
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 3 days ago by 42k • written 15 months ago by • 0
0
votes
4
replies
756
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
12 months ago • updated 11 months ago sreeshmaraj72 • 0
3
votes
7
replies
5.5k
views
error with champ.load
champ
written 6.5 years ago by ▴ 10
0
votes
3
replies
1.8k
views
extract rsids of SNPs using their genomic positions
rsids SNPlocs.Hsapiens.dbSNP150.GRCh38
written 10 months ago by • 0
1
vote
13
replies
11k
views
unable to access index for repository
Bioconductor ConsensusClusterPlus
updated 9 months ago by • 0 • written 17 months ago by • 0
7
votes
38
replies
5.7k
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Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 15 hours ago by ★ 2.0k • written 5.5 years ago by ★ 4.0k
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 6 months ago by 50k • written 12.4 years ago by ★ 13k
2
votes
7
replies
3.0k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
9
votes
11
replies
5.9k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 9 weeks ago by 3.9k • written 2.3 years ago by ▴ 40
2
votes
3
replies
1.1k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 4 months ago by • 0 • written 2.9 years ago by ▴ 470
1
vote
4
replies
2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
6
votes
8
replies
1.2k
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CAGEr bug report: wrong consensus cluster results
CAGEr
updated 10 months ago by ▴ 180 • written 17 months ago by ▴ 30
2
votes
8
replies
560
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
6
votes
5
replies
1.2k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 8 months ago by ▴ 740 • written 9 months ago by ▴ 20
7
votes
18
replies
3.0k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 4 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by • 0
0
votes
6
replies
1.3k
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 10 weeks ago by 50k • written 19.1 years ago by ★ 1.1k
4
votes
3
replies
1.0k
views
WGCNA documentation not available
WGCNA
written 5 months ago by ▴ 10
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by 50k • written 12.0 years ago by ▴ 180
1
vote
5
replies
1.7k
views
rowsum or similar for RleArray?
delayedarray rowsum
written 6.7 years ago by ▴ 180
0
votes
7
replies
1.7k
views
Unable to install RefPlus - R=4.3.1, BiocManager=3.18
Install instal
updated 6 months ago by 65k • written 6 months ago by • 0
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by ▴ 220 • written 6.7 years ago by ▴ 80
2
votes
3
replies
838
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
1,738 results • Page 1 of 35
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Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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