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stringDB PPI network with Log fold change?

ppi string-db rna-seq written 2.6 years ago by abdurehmanb • 0 • updated 2.6 years ago by liux.bio • 350

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Which Ensembl protein id (ENSP) should I use? (Which id is used by string-db)

gene symbol string-db id convert ensembl id written 5.7 years ago by Soheil Jahangiri • 10 • updated 3.4 years ago by mahmoud.s.fahmy • 0

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How to obtain a proof for presence of PP interaction through String API

ppi string-db api written 5.2 years ago by tierprot • 0 • updated 5.2 years ago by Pierre Lindenbaum ♦ 133k

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strange behavior in PPI data of string-db

ppi string-db written 5.4 years ago by aslan.mehrabi • 0 • updated 5.4 years ago by Lars Juhl Jensen ♦ 11k

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Recent Replies

C: Filtering on the minor allele in VCFtools by bjwiley23 • 10
GATK indicates they do this for their [best practices](https://gatk.broadinstitute.org/hc/en-us/a...
C: bigwigs to reads in peaks by pt.taklifi • 60
thank you. that works
C: DESeq2 Dispersion Estimates Curve Poor Fit? by lransom • 0
Sorry, just fixed the image link. I'm trying to compare RNA from exosomes in Disease vs Heathy. I...
C: DESeq2 Dispersion Estimates Curve Poor Fit? by ATpoint ♦ 44k
Can you add code and some context, so what are the samples, in terms of groups, and how many repl...
C: How do i create and populates new sample columns based on values (samples barco by rpolicastro ♦ 3.2k
> P.S.: function pivot_wider seem to be from tidyr package and not dplyr. Nice catch, I edite...
C: How do i create and populates new sample columns based on values (samples barco by andresllucena • 0
I'm sorry, I will correct that. I used values from samples after the first one trying to improve ...
A: How do i create and populates new sample columns based on values (samples barco by rpolicastro ♦ 3.2k
There are values in your example output that don't appear in your example data, but I'll assume y...
A: WGCNA negative values by Kevin Blighe ♦ 69k
A negative FPKM value makes no sense, so, there is something wrong with your data processing step...
A: Identifying 5p and 3p in miRNA isoform expression data from TCGA for feature sel by andresllucena • 0
There is how i solve that: The 3p and 5p strands corresponds to these MIMAT IDs miRNA_region col...
C: Finding sets of Ribo-Seq, mRNA-Seq, and RNC-Seq data by seidel ♦ 7.1k
Have you tried the [GEO search interface][1] with those specific terms? I mean, have you checked ...
A: cellranger count error "Your reference does not contain the expected files, or t by leranwangcs • 20
To answer myself's question: I used a vdj database for my gene expression data. So when I switch ...
C: matching relationship between the old and new coordinate lists after liftover by ATpoint ♦ 44k
Please open a new question and add the code you used. it is unlikely you get help in such an old ...

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