User: anupam sinha

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anupam sinha270
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Posts by anupam sinha

<prev • 27 results • page 1 of 3 • next >
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using ensembl archive in GenomicRanges
... Dear all, Is there any way to use the command makeTranscriptDbFromBiomart (biomart="ensembl",dataset="hsapiens_gene_ensembl",transcript_ids=NULL ) from GenomicRanges package of the Biocunductor so that it can retrieve data from Ensembl release version 62 instead of the current rele ...
genomicranges written 7.9 years ago by anupam sinha270 • updated 7.9 years ago by Paul Leo970
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mapping protein domains to exons
... I have a set of protein sequences (from Biomart ENSEMBL Release 62) of Homo sapiens. On these sequences I have run PFAM-HMMER to find domains on these sequences. I also have coordinates (coding sequence as well as genomic)for the exons that make up these proteins. I want to map the protein domains t ...
biomart written 7.9 years ago by anupam sinha270 • updated 7.9 years ago by Sean Davis21k
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Mapping domains to exons
... Dear all, Apologies for asking a rather vague question. I have a set of Ensembl protein ids/sequences for which I want to find the functional domains and then map this information onto genomic coordinates of the constitutive/normal exons. Is it possible to accomplish this using Bioc ...
written 9.2 years ago by anupam sinha270 • updated 9.2 years ago by Mark Cowley910
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biomaRt problem
... Hi all, I am trying to download dN/dS values for human genes from ensemble using biomaRt. I have used codes from the website : http://www.r-bloggers.com/biomart-and-biomart/ > library("biomaRt") > mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ ensembl") > genes & ...
biomart written 9.4 years ago by anupam sinha270
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Comment: C: exonmap/xmapcore error
... Hi Paul and Crispin, Thanks a lot for your suggetsions. Regards, Anupam On Fri, Jul 23, 2010 at 5:33 AM, Paul Leo wrote: > Hi Crispin, > Great that those changes have been made. Exonmap proved to be very > elegant package and useful package for us. & ...
written 9.4 years ago by anupam sinha270
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Comment: C: exonmap/xmapcore error
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written 9.4 years ago by anupam sinha270
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exonmap/xmapcore error
... Dear all, I have been learning to use exonmap/xmapcore from the tutorial ""Comprehensive analysis of Affymetrix Exon arrays Using BioConductor" . But I have run into some problems. I have installed "xmapcore_homo_sapiens_58" on my system as per instructions . Do I also have to instal ...
exonmap written 9.4 years ago by anupam sinha270 • updated 9.4 years ago by Crispin Miller1.1k
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Comment: C: Regarding ScISI
... Hi Marc, Thanks a lot for your suggestion. It should do perfectly fine. Regards, Anupam On Wed, Jun 23, 2010 at 9:51 PM, Marc Carlson wrote: > Hi Anupam, > > Have you looked at the RpsiXML package? > > http://www.bioconductor.org/packages/release/bioc/html/RpsiXM ...
written 9.5 years ago by anupam sinha270
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Regarding ScISI
... Hi all, While trying to retrieve data regarding protein complexes for Homo sapiens from MIPS came across this package called ScISI. But this package seems to to analyze only the data for yeast proteins. Is there any way to analyze protein complexes from from Humans using ScISI or is there ...
yeast scisi written 9.5 years ago by anupam sinha270 • updated 9.5 years ago by Marc Carlson7.2k
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expression profile
... Dear list, I use the following code to process some cel files I have : > dat<-ReadAffy() > dat_norm<-rma(dat) Background correcting Normalizing Calculating Expression > dat_norm_mat<-exprs(dat_norm) > write.table(dat_norm_mat,"GSE3185.txt",sep="\t",row.names= ...
process written 9.5 years ago by anupam sinha270 • updated 9.5 years ago by James W. MacDonald52k

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