bioc | Data structures and code to read/write BioC XML and Json | Serialization library
kandi X-RAY | bioc Summary
kandi X-RAY | bioc Summary
Data structures and code to read/write BioC XML and Json.
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Top functions reviewed by kandi - BETA
- Verify that the annotation text is correct
- Check if an annotation has an annotation with the given id
- Create a new BioCPassage object
- Adds a sentence to the corpus
- Deserializes a collection from a fp
- Parse a BioCDocument tree
- Parse a BioCCL document tree
- Add a document to the document
- Construct a BioCDocument from a list of passages
- Create a collection of documents
- Deserialize a BioCCL document
- Split a file into multiple documents
- Splits a collection
- Copy all infons from another
- Yields a BioCXML document writer
- Parse a document
- Parse a line_iterator
- Deserialize an annotation
- Load an annotation file
- List all documents in directory
- Yield documents from a directory
- Convert obj to JSON
- Validate a sentence
- Validates a collection
- Write a single document to the server
- Dump an annotation document
bioc Key Features
bioc Examples and Code Snippets
Lines of Code : 22License : Strong Copyleft (CC BY-SA 4.0)
Copy# install
source("http://bioconductor.org/biocLite.R")
biocLite("flowCore")
# convert
library(tools) # for file_path_sans_ext
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(vfrom yahooquery import Ticker
stocks = ['AAU', 'ABEO', 'ABEV', 'ABIO', 'ABUS', 'ACCO', 'ACER', 'ACIU', 'ACOR', 'ACRX', 'ACST', 'ACTG', 'ADAP', 'ADIL', 'ADMA', 'ADMP', 'ADT', 'ADTX', 'ADXS', 'AEG', 'AEHL', 'AEHR', 'AEMD', 'AESE', 'AEY', 'ASSgauss <- selfStart(~ h*exp(-(x-mu)^2/(2*sigma^2)), function(mCall, data, LHS) {
xy <- sortedXyData(mCall[["x"]], LHS, data)
len <- dim(xy)[1]
xyarea <- sum((xy[2:len,2]+xy[1:(len-1),2])*(xy[2:len,1]-xy[1:(len-1),1for stock_name, stock_vars in holdings.items():
print(f'{Fore.GREEN}Draco = AutoTrader | {Fore.RED}{stock_vars["price"]}')
named_list = robjects.r.list(counts=counts)
len13seq <- with(uniprot_data, substr(peptide_sequence, start = ind - 6, stop = ind + 6 ))
library(png)
img <- readPNG(system.file("img", "Rlogo.png", package="png"))
grid::grid.raster(img)
Community Discussions
Trending Discussions on bioc
QUESTION
I'm interested in adding grouping labels above my ggplot bar charts. This feature exists for data visualizations such as phylogenetic trees (in ggtree), but I haven't found a way to do it in ggplot.
I've tried toying around with geom_text, and geom_label, but I haven't had success yet. Perhaps there's another package that enables this functionality? I've attached some example code that should be fully reproducible. I'd like the rating variable to go over the bars of the continents listed (spanning multiple continents).
Any help is greatly appreciated! Thank you!
P.S. pardon all the comments - I was writing a teaching tutorial.
...ANSWER
Answered 2022-Mar-29 at 18:32One approach to achieve your desired result would be via geom_segment. To this end I first prepare a dataset containing the start and end positions of the segments to be put on top of the bars by rating group. Basically this involves converting the discrete locations to numerics.
Afterwards it's pretty straightforward to add the segments and the labels.
QUESTION
Everytime I open a new session in RStudio, I'm greeted with the error message:
...ANSWER
Answered 2022-Mar-28 at 19:26Your user .Rprofile file is loading itself recursively for some reason:
QUESTION
I've spent the day trying to load the appropriate package versions in R that I saved in a renv lockfile.
I used the package RVAideMemoire which is tied in with mixOmics in bioconductor, which can't be loaded automatically using renv::restore().
I followed the steps outlined here to install the appropriate version of bioconductor (3.11) to get moxOmics version 6.12.1.
R how to install a specified version of a bioconductor package?
Unfortunately I ended up with mixOmics version 6.14.1. I attempted to load the earlier version using:
...ANSWER
Answered 2022-Feb-25 at 04:17BiocManager::install() doesn't provide an interface for installing specific versions of a package. The documentation for the version argument states:
version: 'character(1)' Bioconductor version to install, e.g., 'version = "3.8"'. The special symbol 'version = "devel"' installs the current 'development' version.
That is, it relates to the Bioconductor version, not the package version.
That said, you should be able to use renv to install a specific version of the package from Bioconductor. For example:
QUESTION
I'm writing a pipeline in Snakemake that calls an R script. This R script has its own environment, with r-base, r-ggplot2 and r-biocmanager in it. I also need the package ggbio that can be installed with biocmanager. I want to silently install this package when the script is called because I don't want it to flood my terminal. Is there a way to do this? I have this right now, but this still outputs instalment information to the terminal:
ANSWER
Answered 2022-Jan-24 at 20:34If you must install the package quietly you can do:
QUESTION
I'm writing a Snakemake pipeline with a rule that will run an R script. This rule has its own environment that looks like this:
...ANSWER
Answered 2021-Dec-07 at 17:36The YAML shown is substandard (incorrect channel order). But more importantly, it generally does not work well to install anything other than Conda packages in Conda-managed R environments. Fortunately, all Bioconductor packages are on the bioconda channel (usually with a bioconductor- prefix and all lowercase), hence, everything should work perfectly fine with simply:
QUESTION
I'm trying to move the Lolliplot so that all of the labels are on the plot. I am following the vignette here Lolliplot vignette and using the trackViewer library with GRanges but I can't find how to either:
- move the plot down or
- make the labels smaller
Please help!
...ANSWER
Answered 2021-Nov-03 at 00:10If you specify the size of the png you can ensure the plot 'fits', e.g. (from the vignette):
QUESTION
I'm new to flowCore + R. I would like to mimic a histogram plot after gating that can be manually done in FlowJo software. I got something similar but it doesn't look quite right because it is a "density" plot and is shifted. How can I get the x axis to shift over and look similar to how FlowJo outputs the plot? I tried reading this document but couldn't find a plot similar to the one in FlowJo: howtoflowcore Appreciate any guidance. Thanks.
code snippet: ...ANSWER
Answered 2021-May-18 at 09:27The reason that for the "shift" is that the x axis is logarithmic (base 10) in the flowJo graph. To achieve the same result in R, add
QUESTION
I am analyzing some microarray data. For each donor, I have a "before intervention" and an "after intervention" idat file. I have successfully read these into R using the Limma package with the read.idat() function. However, the resulting object only has one column in targets: "IDATfile". I believe that if I was using read.ilmn() I would specify a targets.txt file but I can't see this option when using read.idat(). E.g. in the Limma user guide Illumina example, the targets are "Donor", "Age", and "Cell Type". How do I tell Limma what to put as targets? I would like to have "Donor" and "Intervention".
An example of what I mean:
...ANSWER
Answered 2021-Apr-22 at 04:44If you want to simply edit colnames you can use:
QUESTION
I'm making a call to goseq::goseq. After that, the namespace (if that's the right word) is all upset.
I suppose this goes back to liberal use of library(...) in the package or its dependencies.
How can I prevent the call from masking any objects in my namespace?
...ANSWER
Answered 2021-Mar-12 at 18:40As a proof of concept, this seems to work. Thanks to @KonradRudolph for the comments.
QUESTION
I'm trying to receive stock data for about 1000 stocks, to speed up the process I'm using multiprocessing, unfortunately due to the large amount of stock data I'm trying to receive python as a whole just crashes.
Is there a way to use multiprocessing without python crashing, I understand it would still take some time to do all of the 1000 stocks, but all I need is to do this process as fast as possible.
...ANSWER
Answered 2021-Jan-31 at 19:18Ok, here is one way to obtain what you want in about 2min. Some tickers are bad, that's why it crashes.
Here's the code. I use joblib for threading or multiprocess since it doesn't work in my env. But, that's the spirit.
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Install bioc
You can use bioc like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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