0
votes
2
replies
1.4k
views
how to deal with multiple barcodes/index in the analysis
dnastringset aastringset
8.8 years ago XIA.PAN ▴ 20
0
votes
32
replies
5.7k
views
Identify repetitive sequences in 10kbp promoter region in Mouse
granges short tandem repetitions repeat
8.9 years ago • updated 8.8 years ago mkmb2004 • 0
0
votes
1
reply
1.7k
views
warning message with BSseq function
bsseq
updated 8.8 years ago by ★ 6.5k • written 8.8 years ago by • 0
0
votes
0
replies
1.9k
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Job: Postdoctoral Research Associate, Wellcome Trust-MRC Institute of Metabolic Science (Fixed Term)
genetics job genomics postdoc obesity Job
8.8 years ago njc65 • 0
0
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1
reply
2.8k
views
clusterProlifer: plotGOgraph() error with gseGO() result
clusterprofiler gseGO plotGOgraph() topGO
updated 8.8 years ago by ★ 1.2k • written 8.8 years ago by • 0
0
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1
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1.4k
views
Whole exomes: number of genes, polymorphism
whole exome sequence R bioconductor exome
8.8 years ago bioinf ▴ 10
0
votes
0
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miRNA target prediction tool(package) using R
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8.8 years ago Adam • 0
0
votes
2
replies
1.6k
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DESeq data diagnosis problem (MAplot, dispersion)
deseq2
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by • 0
3
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2
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4.1k
views
Using the ERCC spike as a normalization factor for a custom algorithm
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updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
0
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0
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
8.8 years ago avinash gupta ▴ 130
3
votes
2
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1.3k
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statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 8.8 years ago by ★ 13k • written 8.8 years ago by ▴ 670
1
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3
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Affy exprs multicore processing
affy exprs multicore
8.8 years ago Fiona • 0
3
votes
3
replies
2.3k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 10
2
votes
2
replies
4.5k
views
Can not install deSolve
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updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 10
0
votes
3
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2.4k
views
Problem with mapp ensemble protein ids to entrez ids using org.Hs.eg.db
org.Hs.eg.db entrez gene identifiers ensemble
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
3
votes
2
replies
3.0k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma sva svaseq
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 670
2
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2
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DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2 rlog variancestabilizingtransformation DESeq
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 10
1
vote
1
reply
1.7k
views
Removing Zero Counts from results(dds, contrast=c("condition", "x", "y")) vs removing Zero Counts from Count Table
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updated 8.8 years ago by 43k • written 8.8 years ago by • 0
3
votes
4
replies
3.7k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 10
0
votes
0
replies
1.8k
views
Cytofkit package R: Error in readRDS(pfile)
cytofkit R
8.8 years ago anouk • 0
0
votes
0
replies
1.6k
views
Job: Bioinformaticist, Research Programmer
R genomics statistics Job
8.8 years ago radel • 0
9
votes
11
replies
6.4k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
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updated 8.8 years ago by ▴ 20 • written 9.7 years ago by ▴ 10
0
votes
2
replies
1.9k
views
Missing GenBank accession numbers in the org.Hs.egACCNUM object?
org.hs.eg.db bioconductor
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 30
0
votes
5
replies
2.0k
views
TxDb.Hsapiens.UCSC.hg19.knownGene - Error: subscript contains out-of-bounds indices for some Entrez codes
bioconductor genomicranges homo sapiens
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
0
votes
2
replies
2.1k
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output of propOB function ChemmineR
ChemmineR ChemmineOB ChemmineTools Drug
8.8 years ago elisa.micarelli ▴ 10
3
votes
6
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Strange output from goana()
edger goana
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
1
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4
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Can edgeR be used on GO terms?
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8.8 years ago y.zhang36 • 0
1
vote
2
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DESeq analysis starting from DESeq normalized counts
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updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by • 0
0
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0
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VIPER (Protein Activity Inference) gene expression signature format
VIPER aracne.networks
8.8 years ago user31888 ▴ 30
1
vote
6
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2.5k
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minfi and lumi not available for version 3.3.2
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updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Please help with ballgown problem
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8.8 years ago Sara ▴ 20
0
votes
0
replies
800
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GENESIS examples dataset not found?
bioconductor R
8.8 years ago tjzhou • 0
3
votes
6
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31k
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Designing a contrast in DESEQ
deseq2 design and contrast matrix model matrix
8.8 years ago mrigaya.mehra ▴ 10
0
votes
4
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How to get rid of the AAStrings with a stop codon
aastringset aastring
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 20
3
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7
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Misleading information in reactome.db
reactome.db
8.8 years ago Lluís Revilla Sancho ▴ 760
1
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13
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Similar to Tukey Post hoc after ANOVA
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9.6 years ago • updated 8.8 years ago laianavarromartin ▴ 20
7
votes
8
replies
27k
views
DESeq2 design confusion with three factors
deseq2
updated 8.8 years ago by ▴ 690 • written 8.8 years ago by ▴ 10
0
votes
0
replies
896
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microarray data analysis
microarray
8.8 years ago munirapcu • 0
0
votes
2
replies
2.1k
views
LRT test multiple comparisons
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8.8 years ago laianavarromartin ▴ 20
3
votes
4
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2.1k
views
How often are SNPlocs.Hsapiens.dbSNP-* packages released? and why that time scale?
SNPlocs SNP dbsnp
8.8 years ago Ramiro Magno ▴ 100
0
votes
1
reply
1.9k
views
dendextend: color_branches not working for certain hclust methods
dendextend
8.8 years ago Zach Roe ▴ 10
6
votes
6
replies
7.3k
views
how to extract part of the DNA sequences from a DNAstringset
DNAstringset
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 20
1
vote
5
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2.4k
views
Filtering genes with missing Entrez ID using "nsFilter"
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updated 8.8 years ago by 68k • written 8.8 years ago by • 0
2
votes
1
reply
1.9k
views
Outputting a multiple alignment to file error: could not find function write.XStringSet
msa
updated 8.8 years ago by ▴ 300 • written 8.8 years ago by ▴ 10
0
votes
4
replies
1.9k
views
huex10stv2cdf annotation file needed
cdf microarray affy
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 40
0
votes
1
reply
1.1k
views
P-value in SNP attributes
biomart
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
1
vote
0
replies
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Meta Analysis on CAMERA results
limma camera cohen d meta analysis
8.8 years ago Andy91 ▴ 60
3
votes
4
replies
3.0k
views
DiffBind: error with dba(sampleSheet="samples.csv")
R DiffBind
updated 8.8 years ago by ★ 5.2k • written 8.8 years ago by • 0
0
votes
5
replies
2.2k
views
Extracting all possible annotations between two genomic coordinates
genomes
8.8 years ago KB ▴ 50
2
votes
6
replies
5.3k
views
DESeq2, plotting residuals vs.fitted values
deseq2
updated 8.8 years ago by 43k • written 11.4 years ago by ▴ 70
46,696 results • Page 346 of 934
Recent ...
Replies
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.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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…
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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