0
votes
4
replies
1.9k
views
problem with get_link function
STRINGdb get_link bug
8.1 years ago cristinapasi • 0
0
votes
6
replies
2.0k
views
Unexpected results in the dba.report output files
diffbind
updated 8.1 years ago by • 0 • written 8.3 years ago by • 0
4
votes
2
replies
2.0k
views
How to check if the microarray data is from codelink
codelink microarray
updated 8.1 years ago by 21k • written 8.1 years ago by ▴ 260
1
vote
1
reply
2.5k
views
Job: junior level position in proteomics/data science
proteomics machine learning git docker Job
updated 8.1 years ago by • 0 • written 8.3 years ago by ▴ 70
0
votes
0
replies
1.9k
views
GSEA-class file (.cls) parsing error message
gsea
8.1 years ago snguyen268 • 0
0
votes
0
replies
2.0k
views
replacement has X rows, data has Y rows
crisprseek
8.1 years ago robert_w_link • 0
2
votes
4
replies
3.6k
views
Problem in installing Bioconductor packages due to "IRanges"
lumi methylumi methyAnalysis
8.1 years ago topijush ▴ 10
5
votes
7
replies
2.5k
views
Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R decipher biostrings
updated 8.1 years ago by ▴ 150 • written 8.1 years ago by • 0
0
votes
1
reply
821
views
BioMedR error message
BioMedR
8.1 years ago adham_star50 • 0
0
votes
0
replies
708
views
Error in snpStats::read.pedfile: GeneGeneInter
snpmatrix ped
8.1 years ago GENOMIC_region • 0
0
votes
1
reply
1.2k
views
Gene ontology enrichment
GO Gene ontology
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 50
4
votes
14
replies
8.9k
views
DESeq2: Question about the alpha in summary() and results()
deseq2
updated 3.0 years ago by ▴ 10 • written 8.1 years ago by ▴ 270
0
votes
1
reply
2.0k
views
Identification of Overrepresented Transcription Factor Binding Motifs in the Promoters of a List of DE Genes
HOMER Motif Analysis
updated 8.1 years ago by ★ 1.3k • written 8.1 years ago by • 0
11
votes
14
replies
14k
views
Is there a conceptual difference between vst/rlog transforms and lfcShrink?
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 40
0
votes
5
replies
1.2k
views
Are interaction terms symetrical with regard to the designation of main and secondary effect?
deseq2
8.1 years ago kieran.mace ▴ 40
0
votes
2
replies
1.5k
views
Is it possible to import many .tsr sequence file into R using bio strings for use in DECIPHER?
r biostrings decipher
8.1 years ago reubenmcgregor88 • 0
5
votes
3
replies
3.1k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 10 months ago by ▴ 10 • written 8.1 years ago by ▴ 100
0
votes
0
replies
1.0k
views
Extract info from smc object
PGSEA smc object
8.1 years ago da.de ▴ 30
0
votes
1
reply
2.0k
views
Extract sequences corresponding to TCONS IDs from spliceR
splicer
updated 8.1 years ago by ▴ 120 • written 8.1 years ago by ▴ 20
0
votes
0
replies
1.1k
views
coverage no longer works on GPos objects?
genomicranges gpos
8.1 years ago maltethodberg ▴ 180
0
votes
6
replies
2.8k
views
Add columns to granges object that sum score around range
R Grang r granges rtracklayer
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 20
1
vote
3
replies
1.1k
views
Bios 2018 Toronto, Cananda Information
BioC2018
8.1 years ago destiny_mullens • 0
5
votes
4
replies
4.3k
views
How to use custom cdf "hgu133plus2hsentrezgcdf"?
customcdf affymetrix microarrays hgu133plus2 affy
8.1 years ago rahil ▴ 30
1
vote
2
replies
1.5k
views
Combine multiple sashimis stretching over the same intron
gviz sashimi plots
8.1 years ago Frederik Ziebell ▴ 30
0
votes
0
replies
970
views
[netbenchmark] GeneNet method "Error in .local(object, from, to, ...)"
netbenchmark
8.1 years ago fshodan • 0
2
votes
5
replies
2.6k
views
Colour a phylogenetic tree, based on column in DECIPHER?
r decipher biostrings
updated 8.1 years ago by ▴ 150 • written 8.1 years ago by • 0
10
votes
7
replies
3.5k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 8.1 years ago by 21k • written 8.1 years ago by ▴ 60
2
votes
8
replies
2.7k
views
Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
microarray scan.upc hta2.0
updated 8.1 years ago by ▴ 600 • written 8.1 years ago by • 0
9
votes
2
replies
7.1k
views
log fold change threshold in Deseq2 - using lfcthreshold
lfcthreshold deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 80
0
votes
1
reply
1.6k
views
Base mean count threshold
deseq2 base
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 80
0
votes
5
replies
3.3k
views
getBM in loop
biomart ensembl curl
updated 8.1 years ago by ★ 6.6k • written 8.1 years ago by ▴ 40
0
votes
0
replies
762
views
[netbenchmark] Get a list of Regulators
netbenchmark
8.1 years ago fshodan • 0
0
votes
1
reply
808
views
scater automatically limit gene list size?
scater
8.1 years ago tsofoon • 0
0
votes
0
replies
1.3k
views
Error in move(i, file.path(path, i)) : I could not find the file: 95a5d709-7454-4f76-84b0-a505c32baeb5 ; GDCdownload error
tcgabiolinks gdcdownload tcga-brca
8.1 years ago fawazfebin ▴ 60
1
vote
2
replies
1.7k
views
Differential expression of RNA seq data at gene level (for Beginner)
deseq2 differential gene expression bioconductor
updated 8.1 years ago by ▴ 130 • written 8.1 years ago by • 0
0
votes
1
reply
967
views
Multiple tests in a single deseq object
deseq2
updated 8.1 years ago by ★ 13k • written 8.1 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Problem in working with BiSeq - BSraw
dna methylation biseq
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
0
votes
3
replies
3.5k
views
ERROR: compilation failed for package RSQLite
ubuntu installation
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 70
0
votes
1
reply
1.5k
views
Error with tximport on Kallisto .h5 data.
tximport kallisto bioconductor rnaseq
8.1 years ago srdjan.kasapovic0 • 0
0
votes
5
replies
3.1k
views
enrichGO returning NA
clusterprofiler org.hs.eg.db
updated 8.1 years ago by ★ 1.2k • written 8.1 years ago by • 0
0
votes
5
replies
2.5k
views
error when using ensembldb with a MySQL server
ensembldb rmysql
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 10
0
votes
7
replies
2.0k
views
Installing RnBeads via bioconductor - .onLoad failed in loadNamespace(), call: NULL
package installation .onload
8.1 years ago nicogerstner • 0
0
votes
2
replies
6.2k
views
failing to install the package clusterProfiler in R (version 3.4.1)
clusterprofiler
updated 8.1 years ago by ★ 1.2k • written 8.1 years ago by • 0
5
votes
7
replies
3.2k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 8.1 years ago by ★ 1.2k • written 8.1 years ago by ▴ 60
3
votes
2
replies
1.4k
views
ranges input for GenomicFiles
genomicfiles
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 80
3
votes
5
replies
3.3k
views
GDCdownload error in TCGAbiolinks: Invalid zip name argument
tcgabiolinks gdcdownload unzip
updated 8.1 years ago by ▴ 260 • written 8.1 years ago by ▴ 60
2
votes
3
replies
2.1k
views
Can DESeq2/edgeR perform differential analysis for rRNA?
deseq2 edger rRNA differential gene expression
8.1 years ago r.aprianto ▴ 30
1
vote
4
replies
4.6k
views
Generate 3' UTR and 5' UTR ranges from a gff file
gff genomicranges
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 10
2
votes
2
replies
1.8k
views
Packages employing RangedSummarizedExperiment objects
rangedsummarizedexperiment packages granges iranges
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 60
0
votes
0
replies
1.9k
views
Job: Post-doc / Research Engineer Position: single cell RNAseq R/Perl applications development, IPMC, Sophia Antipolis, France
single cell Job
8.1 years ago Agnes Paquet ▴ 10
46,735 results • Page 290 of 935
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Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice by Gordon Smyth 53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
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A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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