User: Saad Khan

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Saad Khan310
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Posts by Saad Khan

<prev • 126 results • page 1 of 13 • next >
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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 11 weeks ago by Saad Khan310 • updated 11 weeks ago by h.mon21k
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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 7 months ago by Saad Khan310
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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 8 months ago by Saad Khan310
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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 9 months ago by Saad Khan310
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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 21 months ago by Saad Khan310
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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 21 months ago by Saad Khan310
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Cancer data for histone Chip-seq in human and mouse
... Does anyone know of any cancer dataset in mouse and data for the same cancer being available in Human either in GEO or SRA. I tried to look it up in GEO but could not seem to find it would appreciate it if some one knows of the same type of cancer being studied in Human and Mouse for different histo ...
geo sra cancer chip-seq histone written 21 months ago by Saad Khan310 • updated 21 months ago by Ben50
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What does mm10-minimal mean in encode files
... Many encode bam files have labels like mm10-minimal inplace of mm10 sometimes in the metadata file. I was wondering what this is. Is it mm10 with sex and non standard chromosomes removed? Also for one tissue I have multiple bam files for some output type is just alignments while others are labelled ...
metadata mm10-minimal encode written 2.1 years ago by Saad Khan310
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Comment: C: Clustering using codon usage similarity
... How about other more robust methods (r-packages) like K-means, PAM(K-medoids) and mclust etc ...
written 2.2 years ago by Saad Khan310
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How to do gene enrichment analysis using only GO-slim terma
... Hi, Most bioconductor packages use all GO terms. I was wondering if you know of any bioconductor package that does gene enrichment using only GO slim terms thanks ...
go-slim gene enrichment written 2.2 years ago by Saad Khan310 • updated 14 days ago by Explorer60

Latest awards to Saad Khan

Popular Question 6 weeks ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
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 Transcriptional repressors and transcriptional activators
Popular Question 7 months ago, created a question with more than 1,000 views. For How does vcf-stats give snp count
Popular Question 7 months ago, created a question with more than 1,000 views. For Visualizing microRNA expression network
Popular Question 8 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 8 months ago, created a question with more than 1,000 views. For How does vcf-stats give snp count
Popular Question 8 months ago, created a question with more than 1,000 views. For Visualizing microRNA expression network
Popular Question 8 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 8 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 8 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 9 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 20 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 20 months ago, created a question with more than 1,000 views. For How does vcf-stats give snp count
Popular Question 20 months ago, created a question with more than 1,000 views. For Visualizing microRNA expression network
Popular Question 20 months ago, created a question with more than 1,000 views. For How to combine bisulfite sequencing data with Medip seq and/or MRE-seq
Popular Question 20 months ago, created a question with more than 1,000 views. For Quick way to find all the TFBS peak data for mouse and Human in GEO
Popular Question 20 months ago, created a question with more than 1,000 views. For Compare histone modification data with DNA methylation data
Popular Question 20 months ago, created a question with more than 1,000 views. For Cancer gene list enrichment
Popular Question 20 months ago, created a question with more than 1,000 views. For Using CEAS with canine methylation data
Popular Question 22 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators

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