datasets | NCBI Datasets is an experimental resource | Genomics library

by ncbi Jupyter Notebook Version: v14.29.0 License: Non-SPDX

X-Ray Key Features Code Snippets(4)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | datasets Summary

datasets is a Jupyter Notebook library typically used in Artificial Intelligence, Genomics applications. datasets has no bugs, it has no vulnerabilities and it has low support. However datasets has a Non-SPDX License. You can download it from GitHub.

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. NCBI Datasets tools are under active development. Submit feedback by creating a GitHub issue or you may contact NCBI directly with your questions, comments or feature requests.

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Security

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Reuse

Support

datasets has a low active ecosystem.

It has 192 star(s) with 34 fork(s). There are 24 watchers for this library.

There were 3 major release(s) in the last 12 months.

There are 10 open issues and 67 have been closed. On average issues are closed in 270 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of datasets is v14.29.0

Quality

datasets has no bugs reported.

Security

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

License

datasets has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

datasets releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed datasets and discovered the below as its top functions. This is intended to give you an instant insight into datasets implemented functionality, and help decide if they suit your requirements.

Convert_ncbi_datasets_v1_dataset_proto_proto_proto_proto .
Create a new protobi_dataset_descriptor_descriptor_proto_proto_proto_proto .
Convert_ncbi_report_gene_proto_geneur .
Convert_ncbi_v1_v1_report_proto_proto .
Deprecated .
Convert_ncbi_microbigGE_Microbigge_Proto_Proto_proto_proto_proto_proto .
Deprecated .
Convert_ncbi_options_options_proto_openapi_openapi_options_proto_proto_proto .
Deprecated .
Get assembly metadata

Get all kandi verified functions for this library.

datasets Key Features

No Key Features are available at this moment for datasets.

datasets Examples and Code Snippets

Vision Transformer for Small Datasets

pypi

Lines of Code : 30

License : No License

Copy

import torch
from vit_pytorch.vit_for_small_dataset import ViT

v = ViT(
    image_size = 256,
    patch_size = 16,
    num_classes = 1000,
    dim = 1024,
    depth = 6,
    heads = 16,
    mlp_dim = 2048,
    dropout = 0.1,
    emb_dropout = 0.1
)

Distribute datasets from a function .

python

Lines of Code : 78

License : Non-SPDX (Apache License 2.0)

Copy

def distribute_datasets_from_function(self, dataset_fn, options=None):
    # pylint: disable=line-too-long
    """Distributes `tf.data.Dataset` instances created by calls to `dataset_fn`.

    The argument `dataset_fn` that users pass in is an input

Creates a list of Datasets from a function .

python

Lines of Code : 65

License : Non-SPDX (Apache License 2.0)

Copy

def get_distributed_datasets_from_function(dataset_fn,
                                           input_workers,
                                           input_contexts,
                                           strategy,

Sample from datasets .

python

Lines of Code : 61

License : Non-SPDX (Apache License 2.0)

Copy

def sample_from_datasets_v2(datasets,
                            weights=None,
                            seed=None,
                            stop_on_empty_dataset=False):
  """Samples elements at random from the datasets in `datasets`.

  Creat

Community Discussions

Trending Discussions on datasets

Why is this printing twice to my console?

Xarray (from grib file) to dataset

How to print ggplot for multiple tables in this case?

Convert .txt file to .csv , where each line goes to a new column and each paragraph goes to a new row

Find proportion of times each character(A,B,C,D) occurs in each column of a list which has 3 datasets

Dynamically set bigquery table id in dataflow pipeline

ChartJS multiple annotations (vertical lines)

Deeplabv3 re-train result is skewed for non-square images

Drawing SVG Density Chart

In R Shiny, why do my functions not work when using the render UI function but work fine when not using render UI?

QUESTION

Why is this printing twice to my console?

Asked 2021-Jun-16 at 02:48

I am running the following in my React app and when I open the console in Chrome, it is printing the response.data[0] twice in the console. What is causing this?

...

ANSWER

Answered 2021-Jun-16 at 02:48

You have included fetching function in the component as it is, so it fires every time component being rendered. You better to include fetching data in useEffect hook just like this:

Source https://stackoverflow.com/questions/67995505

QUESTION

Xarray (from grib file) to dataset

Asked 2021-Jun-16 at 02:36

I have a grib file containing monthly precipitation and temperature from 1989 to 2018 (extracted from ERA5-Land).

I need to have those data in a dataset format with 6 column : longitude, latitude, ID of the cell/point in the grib file, date, temperature and precipitation.

I first imported the file using cfgrib. Here is what contains the xdata list after importation:

...

ANSWER

Answered 2021-Jun-16 at 02:36

Here is the answer after a bit of trial and error (only putting the result for tp variable but it's similar for t2m)

Source https://stackoverflow.com/questions/67963199

QUESTION

How to print ggplot for multiple tables in this case?

Asked 2021-Jun-15 at 22:10

I have this code which prints multiple tables

...

ANSWER

Answered 2021-Jun-15 at 20:59

So, this is a good opportunity to use purrr::map. You are half way there by applying code to one dataframe.

You can take the code that you have written above and put it into a function.

Source https://stackoverflow.com/questions/67992308

QUESTION

Convert .txt file to .csv , where each line goes to a new column and each paragraph goes to a new row

Asked 2021-Jun-15 at 19:08

I am relatively new in dealing with txt and json datasets. I have a dialogue dataset in a txt file and i want to convert it into a csv file with each new line converted into a column. and when the next dialog starts (next paragraph), it starts with a new row. so i get data in format of

...

ANSWER

Answered 2021-Jun-15 at 19:08

A CSV file is a list of strings separated by commas, with newlines (\n) separating the rows.

Due to this simplistic layout, it is often not suitable for containing strings that may contain commas within them, for instance dialogue.

That being said, with your input file, it is possible to use regex to replace any single newlines with a comma, which effectively does the "each new line converted into a column, each new paragraph a new row" requirement.

Source https://stackoverflow.com/questions/67990813

QUESTION

Find proportion of times each character(A,B,C,D) occurs in each column of a list which has 3 datasets

Asked 2021-Jun-15 at 19:00

I have a list (dput() below) that has 4 datasets.I also have a variable called 'u' with 4 characters. I have made a video here which explains what I want and a spreadsheet is here.

The spreadsheet is not exactly how my data looks like but i am using it just as an example. My original list has 4 datasets but the spreadsheet has 3 datasets.

Essentially i have some characters(A,B,C,D) and i want to find the proportions of times each character occurs in each column of 3 groups of datasets.(Check video, its hard to explain by typing it out)

...

ANSWER

Answered 2021-Jun-09 at 19:00

We can loop over the list 'l' with lapply, then get the table for each of the columns by looping over the columns with sapply after converting the column to factor with levels specified as 'u', get the proportions, transpose, convert to data.frame (as.data.frame), split by row (asplit - MARGIN = 1), then use transpose from purrr to change the structure so that each column from all the list elements will be blocked as a single unit, bind them with bind_rows

Source https://stackoverflow.com/questions/67909583

QUESTION

Dynamically set bigquery table id in dataflow pipeline

Asked 2021-Jun-15 at 14:30

I have dataflow pipeline, it's in Python and this is what it is doing:

Read Message from PubSub. Messages are zipped protocol buffer. One Message receive on a PubSub contain multiple type of messages. See the protocol parent's message specification below:
...

ANSWER

Answered 2021-Apr-16 at 18:49

How about using TaggedOutput.

Source https://stackoverflow.com/questions/67107333

QUESTION

ChartJS multiple annotations (vertical lines)

Asked 2021-Jun-15 at 12:30

i am trying to put 2 vertical lines on a chart.JS chart using the annotations plugin. i am using the following versions: chart.js = 2.8.0 annotations plugin = 0.5.7

here's the JSFiddle

please see my code below:

...

ANSWER

Answered 2021-Jun-15 at 12:30

You have to provide both annotations as object in 1 array, not an array containing objects containing arrays, see example:

Source https://stackoverflow.com/questions/67985768

QUESTION

Deeplabv3 re-train result is skewed for non-square images

Asked 2021-Jun-15 at 09:13

I have issues fine-tuning the pretrained model deeplabv3_mnv2_pascal_train_aug in Google Colab.

When I do the visualization with vis.py, the results appear to be displaced to the left/upper side of the image if it has a bigger height/width, namely, the image is not square.

The dataset used for the fine-tune is Look Into Person. The steps done to do so are:

Create dataset in deeplab/datasets/data_generator.py

...

ANSWER

Answered 2021-Jun-15 at 09:13

After some time, I did find a solution for this problem. An important thing to know is that, by default, train_crop_size and vis_crop_size are 513x513.

The issue was due to vis_crop_size being smaller than the input images, so vis_crop_size is needed to be greater than the max dimension of the biggest image.

In case you want to use export_model.py, you must use the same logic than vis.py, so your masks are not cropped to 513 by default.

Source https://stackoverflow.com/questions/67887078

QUESTION

Drawing SVG Density Chart

Asked 2021-Jun-15 at 05:47

i need to figure out how to get this chart in SVG Format. I almost got it, but i need to perfectly match each sides. When it goes up and down.

...

ANSWER

Answered 2021-Jun-15 at 05:47

Chris W. is 100% correct, using a vector editor like Adobe Illustrator, Inkscape, or Affinity Designer will make your life much easier when working with complex shapes in SVG. However, for simple shapes like this it doesn't hurt to understand the inner-workings of SVG curves. Not only will it help you malke mathematically perfect shapes but your code will also (usually) be much smaller than what an editor will produce.

The example I'm showing here is only one possible approach out of many to accomplishing this shape. I'll explain the procedure and series of commands briefly but I've also included a second copy of your shape with comments and additional shapes to highlight what the control points are doing (this helps me visualize SVG code).

First it moves to a point at x0, y 100 and draws a relative cubic curve (c) whose first control point is right 100px from the start point with no vertical change and whose second control point is right 180px and up 90px from the start point. The following s curve assumes that it will reflect the previous control point of the c curve before it so it only needs it's second control point and end point specified both of which are designated relative to the end point of the c curve and mirror the previous control points of the c curve. The rest is an absolute vertical line (V) to the bottom of the SVG, an absolute horizontal line to the bottom left corner (H) and a Z to close the path. SVG is awesome, hope this helps you.

Source https://stackoverflow.com/questions/67978549

QUESTION

In R Shiny, why do my functions not work when using the render UI function but work fine when not using render UI?

Asked 2021-Jun-14 at 22:51

When running the first "almost MWE" code immediately below, which uses conditional panels and a "renderUI" function in the server section, it only runs correctly when I comment out the 3rd line from the bottom, observeEvent(vector.final(periods(),yield_input()),{yield_vector.R <<- unique(vector.final(periods(),yield_input()))}). If I run the code with this line activated, it crashes and I get the error message Error in [: subscript out of bounds which per my research means it is trying to access an array out of its boundary.

...

ANSWER

Answered 2021-Jun-14 at 22:51

Replace the line you commented out with this

Source https://stackoverflow.com/questions/67975316

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

Vulnerabilities

No vulnerabilities reported

Install datasets

Download and install the NCBI Datasets command-line tools, datasets and dataformat:. For other ways to install, see our command-line tool quickstart.
Download large numbers of genomes by first downloading a dehydrated zip archive and then getting the data in three steps.
Download the dehydrated zip archive
Unzip the downloaded zip archive
Rehydrate to get the data
Download the dehydrated zip archive datasets download genome accession GCF_000001405.39 --dehydrated --filename human_GRCh38_dataset.zip
Unzip the downloaded zip archive unzip human_GRCh38_dataset.zip -d my_human_dataset
Rehydrate to get the data datasets rehydrate --directory my_human_dataset/

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: