User: jack

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jack680
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680
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Germany
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1 month, 2 weeks ago
Joined:
3 years, 6 months ago
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Posts by jack

<prev • 141 results • page 1 of 15 • next >
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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 8 weeks ago by jack680 • updated 8 weeks ago by geek_y8.0k
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6 follow
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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 9 weeks ago by jack680 • updated 9 weeks ago by EagleEye4.7k
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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 12 weeks ago by jack680 • updated 12 weeks ago by EagleEye4.7k
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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 3 months ago by jack680 • updated 3 months ago by Jean-Karim Heriche13k
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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 5 months ago by jack680 • updated 5 months ago by vchris_ngs4.0k
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What does *.* represent after Ensembl transcript name ?
... Hi all, I have expression level of trancripts and most of them contain a number after [.]. As example: ENST00000352998.3 When I search in Ensembl database, instead of **ENST00000352998.3** it shows me **ENST00000352998.7** Does this means that these two are two different transcripts ? or I can s ...
gene bioinformatics ensemble transcript genome written 5 months ago by jack680 • updated 5 months ago by agata88610
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Comment: C: Transcript-Level Versus Gene-Level Go Enrichment Analysis (For Non-Model Organis
... Throughout this post, I couldn't get how is it possible to accociated specific GO term to specific splice isoform of a gene. ...
written 14 months ago by jack680
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How to convert relative coordinate to aboulate coordinate at genome?
... Hi all, I have file that contains following information regarding binding of small RNA into genome. Basically it report the relative start and end of 3'UTR and also binding site of small RNAs in the genome. The coordinate reported here is the relative coordinate and I want to convert these coordina ...
genome R next-gen rna-seq alignment written 17 months ago by jack680
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Comment: C: How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
... It's hg19, but seems that doesn't work ...
written 17 months ago by jack680
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Comment: C: How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
... These are the human transcriptome Ids ...
written 17 months ago by jack680

Latest awards to jack

Popular Question 3 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 4 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 4 months ago, created a question with more than 1,000 views. For Which kind of microRNAs expression are measured in TCGA?
Popular Question 5 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 5 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Great Question 5 months ago, created a question with more than 5,000 views. For How to download Gene annotations.gtf file for Drosophila melanogaster
Popular Question 7 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Epic Question 7 months ago, created a question with more than 10,000 views. For What is the simple way to remove known batch effect from RNA-seq data ?
Great Question 8 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 10 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Student 10 months ago, asked a question with at least 3 up-votes. For what are the best resource to learn Linux bash scripting for Bioinformatics
Great Question 11 months ago, created a question with more than 5,000 views. For What is the best programming language for NGS data analysis pipeline development?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to detect and correct batch effect in NGS expression data ?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to detect and correct batch effect in NGS expression data ?
Student 14 months ago, asked a question with at least 3 up-votes. For what are the best resource to learn Linux bash scripting for Bioinformatics
Popular Question 17 months ago, created a question with more than 1,000 views. For How to detect and correct batch effect in NGS expression data ?
Student 17 months ago, asked a question with at least 3 up-votes. For what are the best resource to learn Linux bash scripting for Bioinformatics
Popular Question 17 months ago, created a question with more than 1,000 views. For How to detect and correct batch effect in NGS expression data ?
Popular Question 17 months ago, created a question with more than 1,000 views. For Looking databases for experimentaly validated miRNA-target interaction
Popular Question 17 months ago, created a question with more than 1,000 views. For Looking databases for experimentaly validated miRNA-target interaction
Popular Question 18 months ago, created a question with more than 1,000 views. For Looking databases for experimentaly validated miRNA-target interaction
Popular Question 18 months ago, created a question with more than 1,000 views. For Looking databases for experimentaly validated miRNA-target interaction
Prophet 18 months ago, created a post with more than 20 followers. For what are the best resource to learn Linux bash scripting for Bioinformatics

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