User: Radhouane Aniba

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Posts by Radhouane Aniba

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Issues installing GenomicAlignments
... Actually, it didnt want to install on a custom directory, but did install on the personal lib one, which is a bit strange to me my sessioninfo  R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.3 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC ...
written 3.5 years ago by Radhouane Aniba240
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Issues installing GenomicAlignments
... Hello I am having same issues installing GenomicAlignments and I am not sure whether it is a bug or it is a problem with the package ? I get this error when I try to install it http://pastebin.com/raw/KLthv7uM Any ideas ? Thanks   ...
genomicalignments written 3.5 years ago by Radhouane Aniba240
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Comment: C: RangedData change space information
... Thank you Michael, You need just to add a solution to the code (just got a message on coderscrowd for an attempt to solve it) Anyway. The problem is that the package TEQC is using this object, I dont know if it is possible to switch between classes and reinject new classes type like RngedData into ...
written 5.6 years ago by Radhouane Aniba240
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RangedData change space information
... Hello all, I am using a pachage from Bioconductor TEQC, and when I load my reads as a bam file, the object created (class RangedData) looks like this RangedData with 6 rows and 1 value column across 84 spaces space ranges | ID | 1 1 [8404005, 8404254] | M00897 ...
cancer teqc written 5.6 years ago by Radhouane Aniba240 • updated 5.6 years ago by Michael Lawrence11k
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Plotting segment of Granges intervals
... Hello I have a Granges object that is like this (used along with ggbio) : GRanges with 6 ranges and 6 metadata columns: seqnames ranges strand | score id highlight | [1] 1 [ 4793, 227744] * | -0.17 DAH115 FALSE [2] ...
written 5.6 years ago by Radhouane Aniba240 • updated 5.6 years ago by Tengfei Yin490
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BSgenome installation error
... Hello everyone I am trying to install the human genome but I am facing an unusual problem here is the error message > biocLite("BSgenome.Hsapiens.UCSC.hg18") Running biocinstall version 2.2.11 with R version 2.7.2 Your version of R requires version 2.2 of BioConductor. Warning in install.packag ...
bsgenome written 7.8 years ago by Radhouane Aniba240 • updated 7.8 years ago by Hervé Pagès ♦♦ 14k
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Are bioconductor packages designed for enrichment analysis affected by KEGG privatization ?
... Hi, Some bioconductor packages like GSEA or GOStats that additionally to GO are designed to measure gene set enrichment using KEGG pathways, still work and give results even after the new paid license and subscription like we all know the story. My question can be discussed in two different ways, ...
pathways gostats written 8.3 years ago by Radhouane Aniba240 • updated 8.3 years ago by Marc Carlson7.2k
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GO enrichement and Ensembl ID
... Hi everyone, I am browsing a lot of BioC packages for GO and KEGG enrichmet, (GOstats etc ..), and almost all of them consider gene lists in EntrezID format, I have EnsemblID gene list, and I am facing the problem of 1 to Many conversion (Same EnsemblID could have many EntreIDs (transcripts) ) Is ...
go written 8.5 years ago by Radhouane Aniba240 • updated 8.5 years ago by Maciej Jończyk720
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GOstats : KEGGHyperGParams error
... Hello, I have a bug with GOstats when I'm trying to use KEGGHyperGParams, here is the error message Error in .nextMethod(.Object = .Object, ...) : invalid names for slots of class "KEGGHyperGParams": conditional I used it the same way I used GOHyperGParams Here is my code > param <- new ...
gostats written 8.5 years ago by Radhouane Aniba240 • updated 8.5 years ago by James W. MacDonald51k
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Comment: C: Gene Lists and Genomes
... Does GOstats give the possibility to calculate the corrected Pvalue in addition to the enrichment Pvalue ? Sometimes in some Cytoscape plugins we find extra pvalues generally Benferroni correction, is it possible with GOstats ? Regards Radhouane 2011/5/5 Marc Carlson > Hi Radhouane, > > ...
written 8.5 years ago by Radhouane Aniba240

Latest awards to Radhouane Aniba

Popular Question 3.5 years ago, created a question with more than 1,000 views. For Plotting segment of Granges intervals
Popular Question 3.5 years ago, created a question with more than 1,000 views. For BSgenome installation error

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