0
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5
replies
2.5k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub orgdb
updated 10.1 years ago by ★ 6.8k • written 10.1 years ago by ▴ 10
1
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4
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6.6k
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using DEseq2 for miRNA differential expression
deseq2
updated 10.1 years ago by ★ 7.9k • written 10.1 years ago by • 0
0
votes
0
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Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
10.1 years ago user31888 ▴ 30
1
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1
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arrayQualityMetrics for outlier detection
arrayQualityMetrics Microarray Outlier
updated 10.1 years ago by ★ 13k • written 10.2 years ago by ▴ 10
0
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6
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Problems installing BiocLite on Fedora 23, R 3.2.2
bioclite gcc install fedora
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 20
0
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1
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1.7k
views
"cannot parse URI" Error for Installing BSgenome.Hsapiens.UCSC.hg19
bioconductor
10.1 years ago Haiying.Kong ▴ 110
0
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2
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2.6k
views
library(clusterProfiler) cnetplot(fixed = F): why can´t I get the color legend?
clusterprofiler tkplot
10.2 years ago • updated 10.1 years ago cristina della beffa ▴ 30
0
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2
replies
1.6k
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oposSOM C binding function error
oposSOM Bellman-Ford bioconductor
10.1 years ago arrigonialberto86 • 0
0
votes
2
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1.6k
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Rtracklayer creating large temp files when importing BigWigs
rtracklayer BigWig
updated 10.1 years ago by ★ 11k • written 10.2 years ago by • 0
0
votes
0
replies
1.6k
views
No significant MVPs with a BH adjusted P-value below 0.05
champ mvp
10.1 years ago maarten.caspers • 0
2
votes
2
replies
1.7k
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snapCGH segmentation fault
snapcgh software error
updated 10.2 years ago by ▴ 70 • written 10.2 years ago by • 0
2
votes
5
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5.8k
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Analysis using a linear model
lmfit
updated 10.2 years ago by 53k • written 10.2 years ago by • 0
2
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4
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2.0k
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DEXSeqHTML doesn't creates plots
dexseq DEXSeqHTML data representation in graphical forms warning message
10.2 years ago Assa Yeroslaviz ★ 1.5k
3
votes
2
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2.1k
views
EBImage read png causes R to crash
ebimage bug
10.2 years ago Henning Redestig ▴ 20
2
votes
1
reply
3.6k
views
PCA from deseq and r function differ
deseq2 pca
updated 10.2 years ago by 43k • written 10.2 years ago by ▴ 80
0
votes
1
reply
1.7k
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Getting data from GEO
affymetrix microarrays GEO geoquery
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
1
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9
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Big data for IRanges: Combining reduce and gaps with dplyr functions
r iranges reduce gaps
10.2 years ago pesquivel • 0
1
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3
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1.9k
views
NAs values when importing BED file using import function
rtracklayer NA BED getseq
10.2 years ago Dimitris Polychronopoulos ▴ 80
2
votes
10
replies
4.1k
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biomaRt package problem
biomart
updated 10.2 years ago by ▴ 800 • written 10.2 years ago by • 0
4
votes
4
replies
3.4k
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DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 20
0
votes
0
replies
1.6k
views
Big data for IRanges: Combining reduce and gaps with dplyr functions
r iranges reduce gaps
10.2 years ago pesquivel • 0
4
votes
4
replies
4.4k
views
Determining direction of logFC in limma
logFC limma
10.2 years ago pt2395 • 0
1
vote
1
reply
1.4k
views
FDR calculation by combineTests in csaw
csaw
updated 10.2 years ago by ★ 29k • written 10.2 years ago by ▴ 20
0
votes
2
replies
2.5k
views
Error with Normalization using (rma) method !!!
normalization rma
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
5
votes
6
replies
4.1k
views
Reactome pathway names from IDs?
biomart reactome reactome.db id
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 680
0
votes
1
reply
2.2k
views
Gene Set Enrichment Analysis with topGO
topGO gene set analysis
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 40
0
votes
3
replies
12k
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trouble using select() to get all GO terms when have duplicate query IDs
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updated 10.2 years ago by 68k • written 10.2 years ago by ★ 2.0k
1
vote
4
replies
1.9k
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DEXSeq Error when calculating Exon Fold-changes
dexseq logfoldchange exon usage
10.2 years ago Assa Yeroslaviz ★ 1.5k
1
vote
1
reply
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DEXSeq: pvalue for multiple conditions
dexseq
updated 10.2 years ago by ★ 1.9k • written 10.2 years ago by • 0
1
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3
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DEXSeqHTML filenames gone wrong
dexseq
updated 10.2 years ago by ★ 1.9k • written 10.6 years ago by ▴ 10
2
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3
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SNP extraction from SNPlocs.Hsapiens.dbSNP144.GRCh38
dbsnp
updated 10.2 years ago by 16k • written 10.2 years ago by • 0
3
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3
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Gene Set Enrichment Analysis with Limma
limma romer gene set analysis
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 40
0
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4
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MakeTxDbFromGFF creates empty object
maketxdbfromgff
updated 10.2 years ago by 16k • written 10.2 years ago by • 0
5
votes
3
replies
1.5k
views
sequenceLayer memory/C code problem?
genomicalignments c gviz
updated 10.2 years ago by 16k • written 10.2 years ago by ★ 2.1k
1
vote
6
replies
11k
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Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
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updated 10.2 years ago by ★ 2.1k • written 10.2 years ago by ▴ 40
16
votes
5
replies
8.7k
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DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
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updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 120
1
vote
2
replies
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Limma multifactorial design
Limma multiple factor design
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 90
0
votes
0
replies
1.4k
views
Background correction arguments in R package GCRMA for microarray pre-processing analysis
gcrma normalization background correction microarray
10.2 years ago svlachavas ▴ 840
1
vote
4
replies
1.7k
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Create a GmapGenome from a FaFile from AnnotationHub
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updated 10.2 years ago by ★ 11k • written 10.2 years ago by ★ 2.1k
1
vote
1
reply
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Write the "map" DataFrame from genotypeToSnpMatrix() to a text file
variantannotation DataFrame snpstats
10.2 years ago TimothéeFlutre ▴ 80
0
votes
2
replies
1.8k
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edge, timeseries analysis, model specification question
edge timecourse fittimeseries
updated 10.2 years ago by • 0 • written 10.2 years ago by • 0
4
votes
9
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2.9k
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How to construct contrasts for a linear model with interactions?
limma contrast linear model
10.2 years ago vedran.franke • 0
0
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1
reply
1.6k
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Upgrading bioconductor - how do I change the contrib.url?
biocinstaller biocupgrade
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
1
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14
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Unable to connect from R 3.2.2
biocinstaller source
10.2 years ago michel.renou • 0
1
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0
replies
2.0k
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Job: Postdoc in Computational Biology
jobs computational biology cancer Job
10.2 years ago Bernd Fischer ▴ 550
5
votes
7
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What does dba.PCA in DiffBind exactly do?
diffbind pca
updated 4.4 years ago by ★ 5.2k • written 10.2 years ago by ▴ 20
0
votes
1
reply
1.5k
views
accounting for gene length with SeqGSEA
goseq SeqGSEA goseq SeqGSEA
updated 10.2 years ago by • 0 • written 12.6 years ago by ▴ 110
0
votes
2
replies
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Problems installing ChipPeakAnno with newest version of R and Bioconductor
chippeakanno installation
10.2 years ago rebecca.halbach • 0
0
votes
2
replies
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BSGenome::getSeq gives error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
bsgenome getseq
updated 10.2 years ago by 25k • written 10.2 years ago by • 0
1
vote
1
reply
1.1k
views
Error with DNAStringSet
biostrings iranges
updated 10.2 years ago by 25k • written 10.2 years ago by • 0
46,721 results • Page 426 of 935
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Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
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This is qq plot and histogram generated before bacon correction ![enter image description here][1] ![enter image description here][2] …
Comment: Ensembl site unresponsive via biomaRt by sebastianenewell • 0
> I think this is an unrelated issue. The original post includes the > message Error: 'curl_parse_url' is not an exported object from > 'na…
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Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
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Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
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A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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