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pathway analysis tools

ipa mirna written 7 months ago by gracie • 0 • updated 7 months ago by Denise - Open Targets • 4.4k

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answer

453

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Ingenuity Pathway Analysis Galaxy Dataset

chip-seq macs2 cuffdiff ipa rna-seq written 12 months ago by benjyrolls • 70

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1.2k

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TCGA data(RPKM) differential gene expression

R tcga ipa rna-seq rpkm written 12 months ago by realnewbie • 10

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809

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how to show others if a pathway is activated ?

proteomics pathway genomic ipa written 20 months ago by Learner • 90 • updated 20 months ago by Biogeek • 260

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1.1k

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IPA Core analysis

ipa rna-seq written 21 months ago by Laura • 0 • updated 21 months ago by vchris_ngs • 4.4k

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863

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Ingenuity Pathway Analysis by Variant Density?

pathway variant ipa density written 22 months ago by anp375 • 120

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8.2k

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What is your opinion on the network score of IPA (Ingenuity Pathway Analysis) analysis?

network ipa written 3.3 years ago by itsunoda • 0 • updated 3.3 years ago by Charles Warden ♦ 5.0k

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3.4k

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Pathway discovery tools (IPA, GENEGO, Pathway studio) for non-pharma analysis ?

pathway ipa genego pathway studio written 3.7 years ago by Brett • 130 • updated 3.7 years ago by cdsouthan • 1.8k

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Recent Replies

A: Get sequences for KEGG by EC and taxa by natasha.sernova • 2.9k
It may be helpful: https://www.biostars.org/p/71737/ https://www.biostars.org/p/55962/ https:/...
C: Display full information about taxa instead of staxids in BLASTn by h.mon ♦ 13k
staxid means Subject Taxonomy ID staxids means unique Subject Taxonomy ID(s), sepa...
C: How to add tdtomato to mouse genome for RNA seq analysis by h.mon ♦ 13k
That is pretty much about it. Just check afterwards if tdtomato is appearing in your counts files.
C: Matching peptides which differ by one letter? by Alex Reynolds ♦ 23k
I added a `break` at the end of a pattern match. That should speed this up a bit, on the assumpti...
A: Matching peptides which differ by one letter? by h.mon ♦ 13k
For a problem like this one, it is unfathomable there is a python answer and not a perl answer. S...
C: Matching peptides which differ by one letter? by Alex Reynolds ♦ 23k
Thanks, should post a fix shortly.
C: Matching peptides which differ by one letter? by h.mon ♦ 13k
I think you are dividing `affinity_file2` by `affinity_file1`, and OP wants the other way around.
A: Matching peptides which differ by one letter? by Alex Reynolds ♦ 23k
#!/usr/bin/env python import sys import re f1 = 'file1.txt' f2 = 'f...
A: hierarchical cluster of drug treatment after correlation analysis by Kevin Blighe ♦ 16k
Check the distribution of your data first by generating a histogram. If it looks like that typic...
C: SNP dataset and Z Score by Ram ♦ 14k
We used to use <0.01% (not more than 1 in 10,000 alleles) as a rare variant cutoff. IMO 1% is ...
A: SNP dataset and Z Score by Kevin Blighe ♦ 16k
Your questions are not a nuisance, so, do not feel bad for asking. In association studies, the u...
A: How to extract from a fasta file, all the protein sequences that have more than by ayixon • 0
Solved. Thank you very much. The perl script worked fine.

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