User: jack

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jack790
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Posts by jack

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How to intersect GWAS data with GTF or any other genomics annotation file?
... Hi, I'm new into GWAS, and I'm trying to intersect a GWAS data with GTF file. Here is the format of the GWAS data that I do have. I would like to intersect these data with GTF file. More specifically, I would like to figure out which SNPs sits where (gene, exon, intergenic, etc) in the genome. Is t ...
genome gwas genetics snp written 4 weeks ago by jack790 • updated 4 weeks ago by Biostar ♦♦ 20
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How to exclude some of breast cancer subtypes just by looking at gene expression?
... Hi, Probably you all know about PAM50 gene signature for breast cancer sub typing. What I'm looking for is the some of small sets of the genes that their expression levels(expressed or not) helps me to exclude some of the breast cancer subtypes (For example, by looking at gene A and gene B expressi ...
genome gene rna-seq cancer written 23 months ago by jack790 • updated 23 months ago by Kevin Blighe51k
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How is it possible that multiple proteins maps to single transcript ids ?
... Hi all, I've downloaded transcript mapping to PDB annotation from [GENECODE][1] [1]: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.metadata.PDB.gz When I look at the table, i see that one transcript id maps to multiple proteins. I was pondering about the reason behind ...
chip-seq sequencing protein rna-seq bioinformatics written 23 months ago by jack790 • updated 23 months ago by Istvan Albert ♦♦ 81k
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Comment: C: How to extract known pathways from protein protein interaction network?
... Either entire or partial is fine. ...
written 24 months ago by jack790
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How to extract known pathways from protein protein interaction network?
... Hi, Given physical protein protein interaction like String and KEGG pathway. I would like to know how many of KEGG pathways or signaling pathways exist in PPI network. Is there any tool to extract known pathways(either entire or partial) from PPI network ? ...
pathway network protein written 24 months ago by jack790
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Computing TPM from normalized read count from DESEQ
... Hey all, I have normalised read count from DESeq2 for miRNA. I would like to compute TPM out of this normalised read count. I was wondering whether would it be possibile to do that ? ...
expression mirna deseq genomics rna-seq written 2.2 years ago by jack790 • updated 2.2 years ago by geek_y10.0k
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Looking for small RNA-seq in single cell
... Hey, I'm looking database that contains small RNA-seq for single cell. Is there any resource to download single cell small RNA-seq ? ...
genome rna-seq sequencing written 2.2 years ago by jack790 • updated 2.2 years ago by EagleEye6.5k
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How to do GO enrichment alanysis at isoform levels ?
... Hi, I would like to do Gene ontology enrichment analysis at isoform leveles(not gene levels). I have table that links each transcripts to SwissProt protein names as follows: ENST00000335137.3 Q8NH21 Q8NH21 ENST00000426406.2 Q6IEY1 Q6IEY1 ENST00000332831.3 Q6IEY1 Q6IEY1 ENST00000342 ...
genome bioinformatics network rna-seq ontology written 2.3 years ago by jack790 • updated 2.3 years ago by EagleEye6.5k
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How to map protein isoform IDs to transcripts IDs ?
... Hi, I would like to map my protein isoform IDs (refseq) to transcript ids. I was wondering whether can someone help me by that ? For example gene ZC3H14 produce following three different isoforms: ZC3H14 NP_079100.2,NP_001153575.1,NP_001313239.1 I would like to map this isoforms to the transcrip ...
proteomics genome rna-seq written 2.3 years ago by jack790 • updated 2.3 years ago by Jean-Karim Heriche21k
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Is they any R package to download processed miRNA expression levle from TCGA?
... Hi all, I would like to download processed miRNA expression levels for different cancers from TCGA. I was wondering whether is there any pakage such that I can use it to download data ? I tried to dowload maually from ICGC, but miRNAs are not annotated. I was wondering whether can you help me wit ...
bioinformatics tca next-gen rna-seq written 2.5 years ago by jack790 • updated 2.5 years ago by ivivek_ngs4.8k

Latest awards to jack

Popular Question 20 days ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 21 days ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 9 months ago, created a question with more than 1,000 views. For What is the best human 3'-UTR annotation?
Great Question 9 months ago, created a question with more than 5,000 views. For What is the simple way to remove known batch effect from RNA-seq data ?
Popular Question 9 months ago, created a question with more than 1,000 views. For How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
Great Question 9 months ago, created a question with more than 5,000 views. For How much of human genome transcribe? How much of transcriptome are non-coding RNAs?
Popular Question 9 months ago, created a question with more than 1,000 views. For Why FPKM value of gene expression profiles are very close to zero?
Popular Question 9 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Great Question 22 months ago, created a question with more than 5,000 views. For What is the simple way to remove known batch effect from RNA-seq data ?
Great Question 22 months ago, created a question with more than 5,000 views. For What is the best programming language for NGS data analysis pipeline development?
Great Question 22 months ago, created a question with more than 5,000 views. For what are the best resource to learn Linux bash scripting for Bioinformatics
Good Question 22 months ago, asked a question that was upvoted at least 5 times. For what are the best resource to learn Linux bash scripting for Bioinformatics
Popular Question 22 months ago, created a question with more than 1,000 views. For What is the best human 3'-UTR annotation?
Popular Question 22 months ago, created a question with more than 1,000 views. For Why FPKM value of gene expression profiles are very close to zero?
Popular Question 22 months ago, created a question with more than 1,000 views. For How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
Popular Question 22 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 22 months ago, created a question with more than 1,000 views. For Where to get human 3'-UTR multiple sequence alignment ?
Great Question 22 months ago, created a question with more than 5,000 views. For How much of human genome transcribe? How much of transcriptome are non-coding RNAs?
Popular Question 22 months ago, created a question with more than 1,000 views. For How to find GO file and do GO enrichment analysis ?
Appreciated 22 months ago, created a post with more than 5 votes. For what are the best resource to learn Linux bash scripting for Bioinformatics

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