cellranger | 10x Genomics Single Cell 3 ' Gene Expression and VDJ Assembly | Genomics library
kandi X-RAY | cellranger Summary
kandi X-RAY | cellranger Summary
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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Top functions reviewed by kandi - BETA
- 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
cellranger Key Features
cellranger Examples and Code Snippets
Community Discussions
Trending Discussions on cellranger
QUESTION
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 23:51So 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.
QUESTION
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 05:49Add this after the YAML and then the method between :::
will work:
QUESTION
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
QUESTION
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 01:15Errors 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.
QUESTION
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 20:35One option would be to make use of geom_hline
instead of geom_polygon
:
QUESTION
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 15:56You 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.
QUESTION
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 07:08A 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,
QUESTION
I am using a cellranger mkref and faced with a strange python problem with GTF (custom gtf file):
...ANSWER
Answered 2021-May-26 at 21:50Python 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.
QUESTION
I am using a cellranger mkref and faced with a strange python problem with GTF (custome gtf):
...ANSWER
Answered 2021-Jun-01 at 20:27I 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
QUESTION
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 09:23This 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
.
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