0
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2
replies
983
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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)
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2.6 years ago Peter Hickey ▴ 760
2
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3
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866
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RNA seq with edgeR with several factors
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2.6 years ago Nathalie ▴ 20
0
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0
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972
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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
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6
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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
820
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Performing pair-wise comparisons for smaller p value analyzing time series data using deseq2
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
1
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3
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3.9k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.6 years ago mollyab12 • 0
0
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1
reply
961
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DESeq2 design formula
DESeq2
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
0
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0
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1.2k
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News: Bioconductor 3.17 is Released!
Packages Release Bioconductor Software
2.6 years ago shepherl 4.2k
2
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1
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1.0k
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edgeR with Successive Differences Contrast Coding?
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updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
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2
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1.3k
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.6 years ago by ▴ 70 • written 2.6 years ago by ▴ 140
1
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0
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946
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News: Bioconductor joins GTN Smörgåsbord online training event, May 22-26, 2023!
Training Bioconductor Event Community News
2.6 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 2.6 years ago by • 0
0
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1
reply
660
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Error: package ‘hgu133plus2’
hgu133plus2
updated 2.6 years ago by 4.2k • written 2.6 years ago by • 0
1
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4
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2.3k
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Merging samples from different sequencing runs
DESeq2
2.7 years ago • updated 2.5 years ago Zainab ▴ 20
0
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1
reply
896
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DEseq2 Single cell data paired design
R
updated 2.6 years ago by ▴ 30 • written 2.6 years ago by • 0
0
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0
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726
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Shifted volcano plot after RankProd
rankp RankProd
2.6 years ago Alessia • 0
0
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2
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
2
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6
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2.0k
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cpg.annotate() in DMRcate error
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updated 2.6 years ago by ▴ 230 • written 2.6 years ago by • 0
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7
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2.3k
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DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
2.6 years ago • updated 2.5 years ago Ti • 0
8
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10
replies
17k
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GSEA preranked analysis downstream of DEseq2
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updated 7 months ago by ★ 5.0k • written 9.4 years ago by ▴ 20
0
votes
4
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1.8k
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Combine RNA-seq
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updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
0
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3
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1.1k
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BioMart Error message when pulling sequences
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updated 2.6 years ago by ★ 6.6k • written 2.6 years ago by • 0
3
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5
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calculate distance to a certain sequence in one gene
SummarizedExperiment Genetics
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
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2
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1.8k
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Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
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 2.6 years ago by 68k • written 2.6 years ago by • 0
1
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1
reply
729
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
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updated 2.6 years ago by 53k • written 2.6 years ago by • 0
1
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0
replies
773
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Typo in GO.db manual reference
GO.db
2.6 years ago RuBBiT0 ▴ 10
0
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3
replies
2.2k
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Error in ImportRData
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written 2.6 years ago by • 0
1
vote
1
reply
1.0k
views
RNA-seq data collected at differnt time points
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
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0
replies
975
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
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2.6 years ago Ortega-C ▴ 10
0
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package ‘Bioconductor’ is not available for Bioconductor version '3.16'
Bioconductor Install
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
2
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2
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FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
2.6 years ago CDSPARKS ▴ 30
1
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3
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tximport error
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updated 2.6 years ago by 43k • written 2.6 years ago by • 0
2
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1
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1.1k
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how diffbind count the reads of each peak in each sample?
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updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by • 0
0
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3
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1.5k
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remving pseudogenes and lncRNA from deseq2 res
filter deseq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
1
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0
replies
1.2k
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News: Biological Data Science summer school 11-16 June in Brixen/Bressanone.
csama
2.6 years ago Wolfgang Huber ★ 13k
0
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2
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1.1k
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WGCNA problem
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updated 2.6 years ago by ▴ 10 • written 2.6 years ago by • 0
0
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1
reply
2.6k
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Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 2.6 years ago by 4.2k • written 2.6 years ago by • 0
0
votes
4
replies
1.4k
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Tximeta error in analysis of downloaded data
tximeta
2.6 years ago 真妃 • 0
4
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6
replies
1.7k
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Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.6 years ago Chris ▴ 20
0
votes
5
replies
2.9k
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enrichKEGG function error
cluster clusterProfiler KEGG
2.6 years ago ruba-mahmoud • 0
0
votes
0
replies
999
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
2.6 years ago Tadeoye ▴ 20
1
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2
replies
1.3k
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summarizeToGene in tximeta causing vastly different results
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updated 2.6 years ago by 43k • written 2.6 years ago by • 0
0
votes
3
replies
2.8k
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getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
written 2.6 years ago by ▴ 70
0
votes
1
reply
745
views
Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
0
votes
1
reply
1.2k
views
Unable to create pd file for ChAMP analysis
ChAMP
updated 17 months ago by • 0 • written 2.6 years ago by • 0
1
vote
0
replies
911
views
Make custom Txdb class objects from Txdb
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2.6 years ago Shreyash ▴ 10
1
vote
3
replies
1.4k
views
fc value in ggmaplot does not correspond to the real lfc value on the plot
DESeq2 ggmaplot
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
3
votes
12
replies
2.9k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 10
46,692 results • Page 54 of 934
Recent ...
Replies
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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