nCov2019 | query stats of infected coronavirus cases

by GuangchuangYu R Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | nCov2019 Summary

nCov2019 is a R library. nCov2019 has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

This package is one of the earliest R packages that designed to query COVID data. It is available since Jan. 2020, at the time there were few data resources available (see our blog post (in Chinese) (Feb. 03, 2020) and another blog post by third party (in English) (Feb. 11, 2020)).

Support

Quality

Security

License

Reuse

Support

nCov2019 has a low active ecosystem.

It has 419 star(s) with 161 fork(s). There are 28 watchers for this library.

It had no major release in the last 6 months.

There are 38 open issues and 31 have been closed. On average issues are closed in 1 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of nCov2019 is current.

Quality

nCov2019 has no bugs reported.

Security

nCov2019 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

nCov2019 does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

nCov2019 releases are not available. You will need to build from source code and install.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of nCov2019

Get all kandi verified functions for this library.

nCov2019 Key Features

No Key Features are available at this moment for nCov2019.

nCov2019 Examples and Code Snippets

No Code Snippets are available at this moment for nCov2019.

Community Discussions

Trending Discussions on nCov2019

snakemake - define input for aggregate rule without wildcards

ggplot2 How to subsetting a value from a DataFrame which have a list of theses?

how to remove part of a dictionaries that are in a list

How to loop through list of dictionaries and insert into sqlite 3

How can I read a tar.gz file directly from a URL into Pandas?

QUESTION

snakemake - define input for aggregate rule without wildcards

Asked 2021-Jun-08 at 15:40

I am writing a snakemake to produce Sars-Cov-2 variants from Nanopore sequencing. The pipeline that I am writing is based on the artic network, so I am using artic guppyplex and artic minion.

The snakemake that I wrote has the following steps:

zip all the fastq files for all barcodes (rule zipFq)
perform read filtering with guppyplex (rule guppyplex)
call the artic minion pipeline (rule minion)
move the stderr and stdout from qsub to a folder under the working directory (rule mvQsubLogs)

Below is the snakemake that I wrote so far, which works

...

ANSWER

Answered 2021-Jun-08 at 15:40

The rule that fails is rule guppyplex, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}.

Looks like the wildcard {barcode} is filled with barcode49/barcode49.consensus.fasta, which happened because of two reasons I think:

First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta, you give an input file which is never described as an output in your workflow. The rule minion has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.

It therefore infers that the {barcode} wildcard somehow has to contain this .consensus.fasta that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.

Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a . (see wildcard_constraints here)

However, the main problem is that catFasta does not find the desired input. I'd suggest changing the output of minion to "nanopolish/{barcode}/{barcode}.consensus.fasta", since the you already take the OUTDIR from the params, that should not hurt your rule here.

Edit: Dummy test example:

Source https://stackoverflow.com/questions/67805295

QUESTION

ggplot2 How to subsetting a value from a DataFrame which have a list of theses?

Asked 2020-Sep-28 at 18:03

That´s for covid data

I have seen a example code from internet to plot a world map wich have a lot of variables. Like name (of the country) ,confirm (cases), suspect, dead, heal, showRate, and the deadRate

But I only know (by the example) how to plot the confirmed cases, and I want to plot dead toll and the deadRate, but I don´t know how to do it

for work with this code you must install these package:

...

ANSWER

Answered 2020-Sep-28 at 18:03

For any reason inside that package (I can not see the settings for the map plot), it is always taking the confirmed serie and plotting it. You can do a trick by replacing the values in confirmed cases by those from death rate and then format the plot. Here the code to hack the plot scheme:

Source https://stackoverflow.com/questions/64104897

QUESTION

how to remove part of a dictionaries that are in a list

Asked 2020-Jul-18 at 22:38

I web scraped a website and inputted the data into an sql3 database. For some reason, there's this black star in front of each name that's not an asterisk. It's one character that goes in front of the name, and I don't want to go in each row of data and erase it by hand because that's tedious, plus when I update the data on the table, the stars are just gonna come back. Does anyone know how to remove the star before it goes into the table? the data I extracted is a list with dictionaries as the elements. Thank you in advance!

...

ANSWER

Answered 2020-Jul-18 at 16:57

That comes from the \u2605 character. The best way to do is to split it from the dict.

Source https://stackoverflow.com/questions/62971221

QUESTION

How to loop through list of dictionaries and insert into sqlite 3

Asked 2020-Jul-18 at 04:09

I'm a beginner at coding so sorry if I made any mistakes. I webscraped a website and got a list of tables from it. I'm trying to insert that data into sqlite 3 using a for loop, and it comes back as an error.

...

ANSWER

Answered 2020-Jul-17 at 23:22

The KeyError: 'Name' error message is indicative that your dictionary does not have a 'Name' Key. You can do several thing to diagnose it;

The easiest thing to do first is to just check the base case, does it have the name entry. I.e.

Source https://stackoverflow.com/questions/62962573

QUESTION

How can I read a tar.gz file directly from a URL into Pandas?

Asked 2020-Jul-02 at 06:45

The dataset I wish to read lives on GitHub as a tar.gz file and is updated every few hours. While I can always download this file, uncompress it, and read from CSV, it would be much better if I can directly read from this URL into a Pandas data frame in a timely manner.

After some Googling, I was able to download the compressed file and then read it as a data frame.

...

ANSWER

Answered 2020-Jul-02 at 06:31

You can use the BytesIO(In-Memory Stream) to keep the data in memory instead of saving the file to local machine.

Also As per the tarfile.open documentation, If fileobj is specified, it is used as an alternative to a file object opened in binary mode for name.

Source https://stackoverflow.com/questions/62689488

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install nCov2019

Get the development version from github:.
get_nCov2019() to query online latest information
load_nCov2019() to get historical data
nCov2019_set_country() to set country options
summary and [ to access data
plot to present data on map
dashboard() to open Shiny app dashboard

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

Find more information at: