cellranger | 10x Genomics Single Cell 3 ' Gene Expression and VDJ Assembly | Genomics library

 by   10XGenomics Python Version: 3.0.2 License: Non-SPDX

kandi X-RAY | cellranger Summary

kandi X-RAY | cellranger Summary

cellranger is a Python library typically used in Artificial Intelligence, Genomics applications. cellranger has no bugs, it has no vulnerabilities and it has low support. However cellranger build file is not available and it has a Non-SPDX License. You can download it from GitHub.

The binaries required to generate Loupe Cell Browser (.cloupe) and Loupe V(D)J Browser files (.vloupe) are not included in this repository or in the binary dependencies package Ranger. The necessary binaries can be obtained from an existing binary version of Cell Ranger by running: cp /path/to/cellranger-3.0.2/cellranger-cs/*/lib/bin/{crconverter,vlconverter} /path/to/open-source-cellranger/lib/bin/.
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            kandi-support Support

              cellranger has a low active ecosystem.
              It has 216 star(s) with 81 fork(s). There are 23 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 70 open issues and 108 have been closed. On average issues are closed in 148 days. There are 10 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of cellranger is 3.0.2

            kandi-Quality Quality

              cellranger has 0 bugs and 0 code smells.

            kandi-Security Security

              cellranger has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              cellranger code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              cellranger 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.

            kandi-Reuse Reuse

              cellranger releases are not available. You will need to build from source code and install.
              cellranger has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions, examples and code snippets are available.
              cellranger saves you 22406 person hours of effort in developing the same functionality from scratch.
              It has 43906 lines of code, 2000 functions and 268 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed cellranger and discovered the below as its top functions. This is intended to give you an instant insight into cellranger implemented functionality, and help decide if they suit your requirements.
            • This callback is called when the barcode is processed
            • Return the single chain
            • Return the CDR sequence
            • Extract quals from VJ
            • Process the raw ilmn data
            • Rename fastq files
            • Call child process
            • Calculate cell barcode coverage
            • Return the clonotype sequence for this variant
            • Run all the features in the input matrix
            • Transform a csv file into sections
            • Parse a sample sheet
            • Setup feature alignment
            • Test the eigenvector
            • Test the PCA test
            • Test the test
            • Return the name of the single chain
            • Return the clonotype sequence
            • Given a bam file return a list of chunk sizes
            • Test the eigenvalues of a sparse matrix
            • Annotate the features in the sequence with the given features
            • Join the dimensions of the dataset
            • Convert bcl to fastq files
            • Run PCA algorithm
            • Split fastq files into chunks
            • Called when the contig_mapping_frac_frac_frac_frac
            • Extract information about the CDR3
            • Evaluate the Proxody
            Get all kandi verified functions for this library.

            cellranger Key Features

            No Key Features are available at this moment for cellranger.

            cellranger Examples and Code Snippets

            No Code Snippets are available at this moment for cellranger.

            Community Discussions

            QUESTION

            Data manipulation in R to be converted into time series data
            Asked 2022-Mar-11 at 23:51

            I am using the url link to download this dataset:

            https://files.hawaii.gov/dbedt/census/census_2020/data/redistricting/PLtable1_2020-county.xlsx

            So in R I am coding it as:

            ...

            ANSWER

            Answered 2022-Mar-11 at 23:51

            So this turned out to be a little more complicated than I first thought, in part because of t(), which is really designed to work with matrices. Fortunately, I was able to find some guidance elsewhere on SO, where I found transpose_df(). Though this works, I imagine this could be cleaned up a bit.

            Source https://stackoverflow.com/questions/71445128

            QUESTION

            Theorem environment not rendering or cross-referencing in distill
            Asked 2022-Jan-05 at 20:23

            I'm trying to write a distill::distill_article blogpost which requires the use of LaTeX math environments e.g. theorem, lemma, proof etc.

            I have tried to follow these instructions and also these instructions but am unable to render the theorem environments whether using LaTeX blocks or rmarkdown blocks.

            I also note that a similar question was asked about specifically using distill::distill_article in bookdown. This fix did not work either. Note that my use-case is to use the bookdown theorem environments inside distill::distill_article, not the other way around.

            Here is a reprex for the issue:

            ...

            ANSWER

            Answered 2022-Jan-03 at 05:49

            Add this after the YAML and then the method between ::: will work:

            Source https://stackoverflow.com/questions/70557340

            QUESTION

            no applicable method for 'prep' applied to an object of class
            Asked 2021-Nov-07 at 21:41

            I am building a custom recipes function and getting an error when I try to prep() the recipe. I get the following error:

            ...

            ANSWER

            Answered 2021-Nov-07 at 21:41

            @importFrom recipes prep bake had to be added to the .R file

            Source https://stackoverflow.com/questions/69852944

            QUESTION

            SVM prediction running fine in my computer but not in R Connect
            Asked 2021-Aug-06 at 04:41

            I’m creating a Shiny app that uses the caret package to do some SVM free-text analysis.

            The app runs fine without any error in my computer. I’m using R x64 4.0.4 and R studio 1.3.1093

            I’m deploying app to an internal enterprise server https://rconnect.xxxx.com/connect/#/apps/####

            This app is deployed in the server and started.
            But when I reach the line where I run the train function:

            ...

            ANSWER

            Answered 2021-Aug-05 at 01:15

            Errors like this in Shiny apps are almost always a result of missing packages, which the logs confirm.

            Turns out in this case I think the missing package is kernlab, which I only found by reading the documentation given here: https://topepo.github.io/caret/train-models-by-tag.html#Support_Vector_Machines. It's a suggested package, not imported, so the command suggested in the comments by heds1 would sort this out.

            Source https://stackoverflow.com/questions/68659043

            QUESTION

            Add circular reference line to polar bar chart in ggplot2
            Asked 2021-Jul-26 at 20:35

            I’m attempting to add a circle using geom_polygon() to add a reference line to radial bar chart. (I know this is not the ideal way to present this data, but it’s not entirely up to me). Following this issue, I can create a nice circle:

            ...

            ANSWER

            Answered 2021-Jul-26 at 20:35

            One option would be to make use of geom_hline instead of geom_polygon:

            Source https://stackoverflow.com/questions/68535993

            QUESTION

            passing a list of variables to recipe in tidymodels causes model error
            Asked 2021-Jul-05 at 15:56

            I have a simple recipe to train a model. My categorical variables are changing over time and sometimes I want a numerical to be treated as categorical (postal code) , so I define a list prior to recipe containing them. (just for the sake of the argument, the list is much longer)

            recipe worked ok, and then trained my model (3 folds) but an error is raised.

            ...

            ANSWER

            Answered 2021-Jul-05 at 15:56

            You definitely were passing the vector of variables correctly to the recipe -- no problem there!

            You were running into other problems with your model fitting. An xgboost model requires all predictors to be numeric, so if you convert something like zip code to factors, you need to then use step_dummy(). If you have something of high cardinality like zip codes, you probably will need to handle new levels or unknown levels as well.

            Source https://stackoverflow.com/questions/68080819

            QUESTION

            get all decimal places using readxlsb and cellranger::cell_limits()
            Asked 2021-Jun-12 at 07:08

            I’m importing some messy data from a range of Excel Binary Workbooks (.xlsb) using readxlsb and cell_limits(), from cellranger. I'm struggling to get enough (all) decimal places.

            This can be illustrated with the dataset that is supplied with the readxlsb package. In the example data, TestBook.xlsb, in sheet Sheet3.1.1, cell E5. This cell contains e^1, with a range of underlying decimal places (2,71828182845905), but is only imported with six decimal places (2.718282).

            In my real life data I have text in a lot of the top lines, which convert the data to charters, like column.4 below, where E5 resides, and raw data with ~16 decimal places. Is there a way I can tweak the code (below) to get all the decimal places without loosing cellranger::cell_limits()?

            ...

            ANSWER

            Answered 2021-Jun-12 at 07:08

            A simple solution could be to force column types to double when importing, i.e. col_types = c("double").

            Beginning by adjusting the shown digits in your tibble,

            Source https://stackoverflow.com/questions/67640325

            QUESTION

            can only concatenate str (not "bytes") to str
            Asked 2021-Jun-06 at 12:19

            I am using a cellranger mkref and faced with a strange python problem with GTF (custom gtf file):

            ...

            ANSWER

            Answered 2021-May-26 at 21:50

            Python 3 treats strings of bytes as a different object from strings of characters. The distinction matters, since a given string of characters can be encoded to bytes in different ways. E.g. in UTF-8, ä is the two bytes c3 a4 (in hex), while in ISO-8859-1 (Latin 1), it's just the single byte e4.

            Like the comment from @Theophrastus says, subprocess.check_output() returns bytes, matching the low-level API. You need to decode it to characters based on what the expected encoding is. E.g.

            Source https://stackoverflow.com/questions/67859031

            QUESTION

            cellranger: how to convert a gtf file to string
            Asked 2021-Jun-01 at 20:27

            I am using a cellranger mkref and faced with a strange python problem with GTF (custome gtf):

            ...

            ANSWER

            Answered 2021-Jun-01 at 20:27

            I encountered the same issue. The problem was in duplicated IDs in my GTF file. Removing those duplicates solved the issue. See the discussion on Cellranger GitHub: https://github.com/10XGenomics/cellranger/issues/125

            Source https://stackoverflow.com/questions/67706086

            QUESTION

            Can you extract defective rows using AssertR in R?
            Asked 2021-May-02 at 08:46

            The example below is a simple one which tries to assert the column y is always positive (y>0). How can I extract the errored data (row 3 with the negative value,into a dataframe maybe, or any convenient object) while allowing the workflow to continue with "cleaned" data?

            ...

            ANSWER

            Answered 2021-Apr-12 at 09:23

            This is tricky, and the answer below doesn't solve this 100%. Now there are a number of different ways assertr lets you handle errors/stops, just see ?error_stop (which is the default).

            You need to not only filter out rows that fail, but also collect them (all) for later inspection.

            Below I wrote my own error handler. It fetches those rows that fail, filter them away, and stores them in the global environment under the varibale my.failed.rows.

            Source https://stackoverflow.com/questions/67053792

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

            Vulnerabilities

            No vulnerabilities reported

            Install cellranger

            Python 2.7.13
            rust 1.28.0
            clang 6.0
            go 1.11
            node v8.11.4

            Support

            We do not provide support for building and running this code. The officially supported release binaries are available at: (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest).
            Find more information at:

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            https://github.com/10XGenomics/cellranger.git

          • CLI

            gh repo clone 10XGenomics/cellranger

          • sshUrl

            git@github.com:10XGenomics/cellranger.git

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