| [ { | |
| "format_version" : "1.0", | |
| "generated_by" : "cytoscape-3.7.1", | |
| "target_cytoscapejs_version" : "~2.1", | |
| "title" : "KEGG style", | |
| "style" : [ { | |
| "selector" : "node", | |
| "css" : { | |
| "font-family" : "Dialog.plain", | |
| "font-weight" : "normal", |
| package: | |
| name: ecell | |
| version: "4.1.4" | |
| build: | |
| number: 0 | |
| skip: True # [win32] | |
| skip: True # [win64 and py<35] | |
| skip: True # [osx and py34] | |
| skip: True # [py26] | |
| skip: True # [py33] |
Here are two extremely simple examples, See http://ecell4.readthedocs.org for more details on running E-Cell4.
Python 2.7.6 (default, Mar 22 2014, 22:59:56)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from ecell4.core import *
| kgml = requests.get('http://rest.kegg.jp/get/mmu04150/kgml').content | |
| soup = BeautifulSoup(kgml, "xml") | |
| entries = soup.find_all('entry') | |
| len(entries) | |
| d = {} | |
| elements = {} | |
| nodes = [] | |
| edges = [] |
Content entered directly below the header but before the first section heading is called the preamble.
| # | |
| # This is a Shiny web application. You can run the application by clicking | |
| # the 'Run App' button above. | |
| # | |
| # Find out more about building applications with Shiny here: | |
| # | |
| # http://shiny.rstudio.com/ | |
| # | |
| library(shiny) |
| library(clusterProfiler) | |
| library(DT) | |
| library(tibble) | |
| pathway <- character(0) | |
| cids <- list() | |
| for(i in 1:length(mset_SMPDB_format_KEGG)) { | |
| row = mset_SMPDB_format_KEGG[[i]] | |
| pathway <- c(pathway, row[[2]]) |
| from __future__ import absolute_import | |
| import pandas as pd | |
| from pandas.api.types import is_numeric_dtype | |
| import numpy as np | |
| import plotly.graph_objs as go | |
| KEGG_PATHWAY_ID = "rn01100" |
| # IPI data from ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release/current/ipi.genes.MOUSE.xrefs.gz | |
| library(tidyverse) | |
| ipi_genes_MOUSE <- read.delim("ipi.genes.MOUSE.xrefs", "\t", escape_double = FALSE, col_names = FALSE, trim_ws = TRUE, skip = 1) | |
| ipi2ncbigene <- ipi_genes_MOUSE %>% select(9,10) %>% | |
| separate(X9, into=c("NCBI_GENEID", "GENE_NAME")) %>% | |
| separate_rows(X10) %>% | |
| filter(X10 != "") %>% | |
| drop_na(NCBI_GENEID) %>% | |
| distinct() |