User: plink_9857

gravatar for plink_9857
plink_985750
Reputation:
50
Status:
Trusted
Location:
United States
Last seen:
1 month, 4 weeks ago
Joined:
4 years, 11 months ago
Email:
m*****@asu.edu

Posts by plink_9857

<prev • 17 results • page 1 of 2 • next >
0
votes
0
answers
209
views
0
answers
Comment: A: Bioconductor PoTRA: Pathways of Topological Rank Analysis
... Hi Everyone, Please try out the PoTRA algorithm and post suggestions here about what features would would like to have added to it. Its a really great, easy program for generating ranked KEGG pathways with mRNA data. Thanks. Home: https://www.bioconductor.org/packages/release/bioc/html/PoTRA.html ...
written 8 weeks ago by plink_985750
0
votes
0
answers
209
views
0
answers
Comment: A: Bioconductor PoTRA: Pathways of Topological Rank Analysis
... Hi Everyone, Don't forget to try PoTRA for mRNA pathway analysis. It's very easy to use. Please post questions and I will help you if you need it. Thanks. ...
written 9 weeks ago by plink_985750
0
votes
0
answers
209
views
0
answers
Tool: Bioconductor PoTRA: Pathways of Topological Rank Analysis
... **Bioconductor PoTRA: Pathways of Topological Rank Analysis** The PoTRA analysis is based on topological ranks of genes in biological pathways. PoTRA can be used to detect pathways involved in disease (Li, Liu & Dinu, 2018). We use PageRank to measure the relative topological ranks of genes in ...
bioconductor pathyways disease potra tool written 3 months ago by plink_985750
0
votes
1
answer
169
views
1
answer
Deformed VCF header and VEP
... I am using VEP to annotate VCF files. One VCF file has a deformed header that does not include the VCF format version information thus causing an error message to generate from VEP. How do I fix the deformed VCF header? I don't know who generated it, therefore, I can't get extra help from its source ...
vcf annotation vep written 5 months ago by plink_985750 • updated 5 months ago by Astrid_Ensembl330
1
vote
0
answers
475
views
0
answers
Subnetworks for Genomic Data
... What algorithms are you all using these days to build subnetworks from genomic data? ...
omics networks written 2.1 years ago by plink_985750
0
votes
0
answers
787
views
0
answers
igraph PoTRA error
... I need help troubleshooting the PoTRA program (which depends on igraph). The PoTRA's program functions, workspace file, etc can be found here: See the error message below. https://github.com/GenomicsPrograms/PoTRA/tree/master/PoTRA%20Code After running the following code: First paste the function ...
igraph potra written 2.5 years ago by plink_985750 • updated 2.5 years ago by genomax90k
0
votes
0
answers
608
views
0
answers
miR2Pathway and finite observations
... **I am using the miR2Pathway package and have encountered an error message and warning messages that I need help troubleshooting**. The finite observations warning is interesting to me, since it alludes to there being too few mirna listed. The input file contains 1,046 miRNAs that are being analyze ...
pathway R mirna written 2.5 years ago by plink_985750 • updated 2.5 years ago by genomax90k
0
votes
0
answers
693
views
0
answers
scRNA gene scores/ranking computational tool
... I'm trying to find a good tool to perform gene scoring or gene ranking with scRNA data. Any recommendations? ...
scrna gene scores gene ranks written 3.1 years ago by plink_985750
4
votes
1
answer
1.4k
views
5 follow
1
answer
CNVkit GRCh38 tumor-normal pair
... I recently tried to use CNVKit in DNAnexus. CNVKit requires a tumor and normal bam, reference fasta (I used GRCh38 from Gencode) and a target or bait file. I tried to use the hg38 bed file from ucsc (hg38_GENCODE_v23_basic.bed), but the CNVKit program did not find common chromosome names between th ...
wes tcga grch38 cnv bed written 3.2 years ago by plink_985750 • updated 3.2 years ago by Eric T.2.6k
1
vote
1
answer
1.4k
views
1
answer
BWAKIT HLA Analysis
... Hi- I recently used BWAKIT for HLA typing. But am having difficulty finding information that can help me interpret the output. Here are my questions and links to somewhat helpful sites. 1) What are the headers for the output file: out.hla.top? (Snippet from my out.hla.top file): HLA-A*29:02: ...
analysis hla bwakit written 3.9 years ago by plink_985750 • updated 3.9 years ago by drmaly220

Latest awards to plink_9857

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Perl script for reformatting a plink/seq output file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For GATK Haplotype Caller
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Perl script for reformatting a plink/seq output file
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Perl script for reformatting a plink/seq output file
Popular Question 3.1 years ago, created a question with more than 1,000 views. For GATK Haplotype Caller
Student 3.9 years ago, asked a question with at least 3 up-votes. For Perl script for reformatting a plink/seq output file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 847 users visited in the last hour