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0
votes
7
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2.9k
views
Filter Out Low Read Counts
deseq2 r
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
vote
6
replies
13k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r rnaseq complexHeatmap annotation
updated 5.5 years ago by ▴ 290 • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
2
votes
0
replies
864
views
Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
5.5 years ago hamza_karakurt ▴ 60
0
votes
1
reply
1.2k
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.3k
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler Bioconductor R DEGs
5.5 years ago tpm • 0
0
votes
0
replies
1.3k
views
reactomePA error input file
r reactomePA enrichment
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
2
votes
7
replies
1.9k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
5
replies
2.1k
views
Error with using getBM function in biomaRt
go r software error R biomaRt
5.5 years ago morteza.aslanzadeh ▴ 30
0
votes
2
replies
3.5k
views
Normalisation of rlog and VSD transformation
deseq2 rna-seq R
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
1
vote
3
replies
2.7k
views
Pairwise comparison of multiple groups with different base
deseq2 rna-seq r
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
0
votes
5
replies
2.2k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
0
votes
1
reply
1.0k
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq R methylation
5.6 years ago AishaD • 0
5
votes
2
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2.9k
views
How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
1
vote
1
reply
2.4k
views
Differential expression on Nanostring normalised protein data
R Differential expression
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
3
votes
4
replies
1.4k
views
Why BiocManager try to reinstall dependencies already installed?
R
updated 5.6 years ago by ★ 3.4k • written 5.6 years ago by • 0
6
votes
3
replies
2.2k
views
Multi-level experiments in Limma
limma rnaseq r
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
how to design probes using decipher
R decipher
5.6 years ago hoonhuiyi • 0
0
votes
0
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817
views
How to generate custom MS database using CustomProDB?
r proteomics
5.6 years ago nattzy94 ▴ 20
3
votes
2
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3.6k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
1
vote
1
reply
2.2k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
3
votes
3
replies
7.4k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 2.5 years ago by ★ 4.1k • written 5.6 years ago by • 0
0
votes
1
reply
1.9k
views
matrix for multiple files
r
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
1
vote
1
reply
528
views
How to create a simple design matrix for limma
limma r
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
votes
0
replies
1.2k
views
Export Results from BatchQC Shiny App
BatchQC RNA-seq R Shiny batch-effect
5.6 years ago manninm • 0
2
votes
3
replies
2.3k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 5.6 years ago by 68k • written 5.7 years ago by • 0
0
votes
0
replies
856
views
Help about MSstats in skyline
Skyline.MS MSstats R
5.7 years ago pokhf123 • 0
0
votes
3
replies
929
views
DESeq2 library problem
R deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
2
replies
1.8k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
3
votes
4
replies
2.2k
views
Can't install packages on R or via Bioconductor
R installation packages annotatr biocmanager
5.7 years ago dakarai_esgdaille ▴ 10
0
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2
replies
2.2k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 5.7 years ago by ★ 1.1k • written 5.8 years ago by • 0
0
votes
1
reply
947
views
Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?
limma R microarray timepoint affy
updated 5.7 years ago by 4.2k • written 5.7 years ago by • 0
0
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1
reply
1.3k
views
R circlize package problem with drawing histogram
circlize R Circos Plots
5.7 years ago marvel479 • 0
2
votes
1
reply
1.9k
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 30
0
votes
2
replies
1.1k
views
New package function redistribution
package license C R
5.7 years ago adam.eleni1 • 0
0
votes
2
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586
views
tximport names must be the same length as the vector
r
updated 3.7 years ago by • 0 • written 5.7 years ago by • 0
0
votes
1
reply
3.7k
views
Installation Path Not Writeable
R BioConductor
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
7
votes
16
replies
5.1k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 12 months ago by • 0 • written 5.7 years ago by ▴ 120
1
vote
1
reply
1.4k
views
Trouble using affy library
software error R microarray affy
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
3
replies
2.1k
views
DESeq2 - cannot find function?
deseq2 r software error
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
1
reply
866
views
DiffBind t-statistic values
r DiffBind ATAC
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by • 0
2
votes
4
replies
1.8k
views
Weird error in Rstudio trying to retreive and load genomic data from external databases
R software error Bioconductor
5.8 years ago svlachavas ▴ 840
0
votes
6
replies
3.1k
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 20
0
votes
0
replies
862
views
Plot seperate Schoenfeld plots for different clusters/subtypes
R survival analysis
5.8 years ago omarrafiqued ▴ 50
3
votes
6
replies
4.6k
views
Including multiple covariates in edgeR
edger R limma
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
3
votes
1
reply
1.7k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 5.8 years ago by 53k • written 6.2 years ago by ▴ 50
0
votes
4
replies
3.7k
views
extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons R
updated 4.3 years ago by ▴ 60 • written 5.8 years ago by ▴ 40
0
votes
2
replies
1.5k
views
R: Error in pedigree(id, momid, dadid, sex): object "id" not found
R kinship2 pedigree
updated 5.8 years ago by 4.2k • written 5.8 years ago by • 0
1
vote
2
replies
904
views
R error: Installation path not writeable
R
5.8 years ago sara.aglantarek • 0
0
votes
0
replies
1.3k
views
gage function problem in R
gage R kegg pathview
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1,163 results • Page 6 of 24
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
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…
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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