User: jack

gravatar for jack
jack800
Reputation:
800
Status:
Trusted
Location:
Germany
Last seen:
2 months ago
Joined:
5 years, 10 months ago
Email:
a************@gmail.com

Posts by jack

<prev • 149 results • page 1 of 15 • next >
0
votes
0
answers
115
views
0
answers
How to compute differential genome wide enrichment of specific histone marks from chip-seq data
... Hi, I have chip-seq data for different histone marks between different conditions. I would like to look at the differential genome-wide loss of specific histone signals. What is the best way to compute and visualize such a signal and make a kind of general statement? I want something beyond of diff ...
chip-seq written 9 weeks ago by jack800
0
votes
0
answers
124
views
0
answers
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 months ago by jack800 • updated 4 months ago by Biostar ♦♦ 20
9
votes
1
answer
2.1k
views
10 follow
1
answer
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 2.2 years ago by jack800 • updated 2.2 years ago by Kevin Blighe54k
0
votes
2
answers
461
views
2
answers
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 2.2 years ago by jack800 • updated 2.2 years ago by Istvan Albert ♦♦ 82k
0
votes
1
answer
1.1k
views
1
answers
Comment: C: How to extract known pathways from protein protein interaction network?
... Either entire or partial is fine. ...
written 2.3 years ago by jack800
1
vote
1
answer
1.1k
views
1
answer
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 2.3 years ago by jack800
3
votes
1
answer
3.8k
views
1
answer
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 2.5 years ago by jack800 • updated 2.5 years ago by geek_y10k
2
votes
2
answers
1.3k
views
6 follow
2
answers
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 2.5 years ago by jack800 • updated 2.5 years ago by EagleEye6.6k
2
votes
1
answer
740
views
1
answer
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 2.6 years ago by jack800 • updated 2.6 years ago by EagleEye6.6k
0
votes
1
answer
814
views
1
answer
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 2.6 years ago by jack800 • updated 2.6 years ago by Jean-Karim Heriche21k

Latest awards to jack

Epic Question 3 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 ?
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 UCSC Isoform ID conversion
Popular Question 12 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 12 months ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Popular Question 12 months ago, created a question with more than 1,000 views. For What is the best human 3'-UTR annotation?
Great Question 12 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?
Great Question 12 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 12 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 2.1 years 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 2.1 years ago, created a question with more than 1,000 views. For Where to get human 3'-UTR multiple sequence alignment ?
Great Question 2.1 years ago, created a question with more than 5,000 views. For what are the best resource to learn Linux bash scripting for Bioinformatics
Great Question 2.1 years 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 2.1 years 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 2.1 years ago, created a question with more than 1,000 views. For What is the best human 3'-UTR annotation?
Popular Question 2.1 years 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 2.1 years ago, created a question with more than 1,000 views. For How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For UCSC Isoform ID conversion
Good Question 2.1 years ago, asked a question that was upvoted at least 5 times. For what are the best resource to learn Linux bash scripting for Bioinformatics
Appreciated 2.1 years ago, created a post with more than 5 votes. For what are the best resource to learn Linux bash scripting for Bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2075 users visited in the last hour