User: Saad Khan

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Saad Khan330
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330
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Posts by Saad Khan

<prev • 130 results • page 1 of 13 • next >
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Comment: C: Merging variant calls of whole exome and RNA-seq
... @archie This probably does not do what I want. I only need to merge the RNA and exome vcf file so that I can make a consensus fasta file from it using FastaAlternateReferenceMaker in GATK. ...
written 3 months ago by Saad Khan330
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Merging variant calls of whole exome and RNA-seq
... Hi, I have many samples for which I have whole-exome and corresponding RNA-seq data I have already done GATK variant calling using their best practices and recommendations. Now I would like to merge the variants from the two approaches. I know the merging may not be straightforward because of RNA-s ...
snvs gatk variants rna-seq indels written 3 months ago by Saad Khan330 • updated 3 months ago by archie70
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Comment: C: Negative dataset selection
... Hi @Jean-Karim Heriche I have edited the question to provide more information. Looking forward to your reply. Thanks! ...
written 4 months ago by Saad Khan330
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Negative dataset selection
... Hi, I am working on a classification problem using a sequence data. I have the positive data which belongs to a gene region I also have negative data which I have selected based upon the most common 5 nucleotides in the center. It seems like my model is over fitting and giving me very high accuracy ...
machine-learning sequence classification rna dna written 4 months ago by Saad Khan330
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Which tool to use to get all citations of a pmid paper?
... Hi, I have thousands of pmid which are associated with a disease. For each pmid I need to find how many times it has been cited in a publication in order to assign importance to that particular pmid. I was wondering what available methods/tools are there that can give me this information. I have tr ...
entrez eutils efetch written 8 months ago by Saad Khan330 • updated 8 months ago by h.mon26k
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Tool for generating Physicochemical properties from sequence of RNA/DNA
... Hi, I am trying to generate some machine learning features for my prediction problem. I was planning to use physicochemical properties of the sequence of nucleotide for doing that. I was wondering what tools are available that could help me do that. Thanks! ...
mrna physicochemical properties sequence dna written 14 months ago by Saad Khan330
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Comment: C: Most genes with entrez id in KEGG database don't have a pathway assigned. Is the
... We did contrast mining between cases and controls for a neurological disorder in which we found SNP associations between a list of gene pairs. We want to do module enrichment for those gene pairs. Many of the genes identified in these gene pairs do not have a reactome_id or kegg pathway id associate ...
written 15 months ago by Saad Khan330
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Most genes with entrez id in KEGG database don't have a pathway assigned. Is there a tool already available that uses textmining to assign pathway to genes.
... Hi, I was working with bioconductor package KEGGREST in trying to find gene 2 pathway mappings. In Kegg according to KEGGREST there are only 7364 genes which are present in the 317 pathways. There are a total of 39556 genes in KEGG I was wondering how can I find pathways for the rest of the genes ...
keggrest reactome kegg written 15 months ago by Saad Khan330
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Comment: C: Protein protein interaction conservation scores
... I am more interested in looking at protein interaction conservation. Which I believe would be similar for species like human and mice for which interactome data is well defined.There has been some research in the area where people have used/calculated PPI similarity measure but these were done using ...
written 2.2 years ago by Saad Khan330
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Protein protein interaction conservation scores
... Hi, I am wondering if there is a resource that can give me protein protein interaction conservation score for a pair of proteins that have orthologues in two species in this case mouse and human and if someone can point me to it. ...
conservation ppi scores written 2.2 years ago by Saad Khan330

Latest awards to Saad Khan

Popular Question 9 weeks ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 12 weeks ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 4 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 4 months ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 4 months ago, created a question with more than 1,000 views. For How does vcf-stats give snp count
Popular Question 4 months ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Popular Question 7 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Great Question 7 months ago, created a question with more than 5,000 views. For small RNA-seq pipelines
Popular Question 7 months ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Popular Question 7 months ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Popular Question 13 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 13 months ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Popular Question 13 months ago, created a question with more than 1,000 views. For How does vcf-stats give snp count
Great Question 13 months ago, created a question with more than 5,000 views. For small RNA-seq pipelines
Popular Question 13 months ago, created a question with more than 1,000 views. For Visualizing microRNA expression network
Popular Question 14 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 14 months ago, created a question with more than 1,000 views. For Visualizing microRNA expression network
Popular Question 14 months ago, created a question with more than 1,000 views. For How does vcf-stats give snp count
Popular Question 14 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 14 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 15 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 15 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators

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