1
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4
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8.8k
views
Error loading impute(): '/usr/lib/libgfortran.5.dylib' (no such file)
Install impute
updated 2.6 years ago by • 0 • written 3.9 years ago by • 0
0
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1
reply
1.5k
views
DESeq2 Results and Alpha questions
DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
1
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2
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915
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Different regions for normalisation
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2.6 years ago msrch • 0
0
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0
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1.2k
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package ‘riboSeqR’ is not available for this version of R
Bioconductor riboSeqR
2.6 years ago Javier • 0
0
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2
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1.2k
views
Why my log2fcs are too high?
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2.7 years ago • updated 2.6 years ago paria.alipour • 0
0
votes
1
reply
984
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
2.6 years ago Grace • 0
0
votes
2
replies
1.7k
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Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.6 years ago Yijing • 0
0
votes
2
replies
989
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Unable to access Git links.
Source flowCore Repository git
updated 2.6 years ago by 4.2k • written 2.6 years ago by • 0
0
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0
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1.2k
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Job: Bioinformatics Research Assistant at WEHI (Melbourne, Australia)
JobPosting
2.6 years ago Peter Hickey ▴ 760
2
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3
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872
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RNA seq with edgeR with several factors
RNAseq factors
2.6 years ago Nathalie ▴ 20
0
votes
0
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978
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News: Include your Bioconductor tutorial in Smörgåsbord 2023, May 22-26!
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2.6 years ago Maria Doyle ▴ 110
0
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6
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1.9k
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convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 2.6 years ago by • 0 • written 4.3 years ago by • 0
0
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1
reply
827
views
Performing pair-wise comparisons for smaller p value analyzing time series data using deseq2
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.7 years ago by • 0
1
vote
3
replies
3.9k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.7 years ago • updated 2.6 years ago mollyab12 • 0
0
votes
1
reply
968
views
DESeq2 design formula
DESeq2
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
0
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0
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1.2k
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Packages Release Bioconductor Software
2.7 years ago shepherl 4.2k
2
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1
reply
1.1k
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting contrastCoding edger ExperimentalDesign expressionDifferences
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
votes
2
replies
1.3k
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.7 years ago by ▴ 70 • written 2.7 years ago by ▴ 140
1
vote
0
replies
955
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News: Bioconductor joins GTN Smörgåsbord online training event, May 22-26, 2023!
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2.7 years ago Maria Doyle ▴ 110
0
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3
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1.3k
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edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 2.6 years ago by 53k • written 2.7 years ago by • 0
0
votes
1
reply
664
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Error: package ‘hgu133plus2’
hgu133plus2
updated 2.7 years ago by 4.2k • written 2.7 years ago by • 0
1
vote
4
replies
2.3k
views
Merging samples from different sequencing runs
DESeq2
2.7 years ago • updated 2.6 years ago Zainab ▴ 20
0
votes
1
reply
905
views
DEseq2 Single cell data paired design
R
updated 2.7 years ago by ▴ 30 • written 2.7 years ago by • 0
0
votes
0
replies
731
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Shifted volcano plot after RankProd
rankp RankProd
2.7 years ago Alessia • 0
0
votes
2
replies
1.4k
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 2.6 years ago by • 0 • written 2.7 years ago by • 0
2
votes
6
replies
2.0k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.7 years ago by ▴ 230 • written 2.7 years ago by • 0
0
votes
7
replies
2.3k
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DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
2.7 years ago • updated 2.6 years ago Ti • 0
8
votes
10
replies
17k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 7 months ago by ★ 5.0k • written 9.4 years ago by ▴ 20
0
votes
4
replies
1.8k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
0
votes
3
replies
1.2k
views
BioMart Error message when pulling sequences
biomaRt bioma
updated 2.7 years ago by ★ 6.6k • written 2.7 years ago by • 0
3
votes
5
replies
1.7k
views
calculate distance to a certain sequence in one gene
SummarizedExperiment Genetics
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
votes
2
replies
1.8k
views
Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
2.7 years ago • updated 2.6 years ago arisarkar88 ▴ 40
0
votes
1
reply
1.7k
views
In .local(object, test.stat, ...) : No enrichment can pe performed - there are no feasible GO terms!
topGO
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
1
vote
1
reply
734
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
1
vote
0
replies
780
views
Typo in GO.db manual reference
GO.db
2.7 years ago RuBBiT0 ▴ 10
0
votes
3
replies
2.3k
views
Error in ImportRData
dplyr IsoformSwitchAnalyzeR
written 2.7 years ago by • 0
1
vote
1
reply
1.0k
views
RNA-seq data collected at differnt time points
DESeq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
votes
0
replies
983
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
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2.7 years ago • updated 2.6 years ago Ortega-C ▴ 10
0
votes
1
reply
5.7k
views
package ‘Bioconductor’ is not available for Bioconductor version '3.16'
Bioconductor Install
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
2
votes
2
replies
3.9k
views
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
2.7 years ago CDSPARKS ▴ 30
1
vote
3
replies
1.7k
views
tximport error
tximport r
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
2
votes
1
reply
1.1k
views
how diffbind count the reads of each peak in each sample?
diffbind DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
votes
3
replies
1.5k
views
remving pseudogenes and lncRNA from deseq2 res
filter deseq2
updated 2.6 years ago by 43k • written 2.7 years ago by • 0
1
vote
0
replies
1.2k
views
News: Biological Data Science summer school 11-16 June in Brixen/Bressanone.
csama
2.7 years ago Wolfgang Huber ★ 13k
0
votes
2
replies
1.1k
views
WGCNA problem
WGCNA
updated 2.7 years ago by ▴ 10 • written 2.7 years ago by • 0
0
votes
1
reply
2.7k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 2.7 years ago by 4.2k • written 2.7 years ago by • 0
0
votes
4
replies
1.4k
views
Tximeta error in analysis of downloaded data
tximeta
2.7 years ago • updated 2.6 years ago 真妃 • 0
4
votes
6
replies
1.7k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.7 years ago Chris ▴ 20
0
votes
5
replies
2.9k
views
enrichKEGG function error
cluster clusterProfiler KEGG
2.7 years ago • updated 2.6 years ago ruba-mahmoud • 0
0
votes
0
replies
1.0k
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
2.7 years ago Tadeoye ▴ 20
46,699 results • Page 54 of 934
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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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