RSEM | RSEM: accurate quantification of gene and isoform expression from RNA-Seq data | Genomics library

by deweylab C++ Version: v1.3.3 License: GPL-3.0

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

kandi X-RAY | RSEM Summary

RSEM is a C++ library typically used in Artificial Intelligence, Genomics applications. RSEM has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

[Prior-enhanced RSEM (pRSEM)] uses complementary information (e.g. ChIP-seq data) to allocate RNA-seq multi-mapping fragments. We included pRSEM code in the subfolder pRSEM/ as well as in RSEM’s scripts rsem-prepare-reference and rsem-calculate-expression.

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Quality

Security

License

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Support

RSEM has a low active ecosystem.

It has 344 star(s) with 109 fork(s). There are 21 watchers for this library.

It had no major release in the last 12 months.

There are 106 open issues and 61 have been closed. On average issues are closed in 79 days. There are 6 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of RSEM is v1.3.3

Quality

RSEM has 0 bugs and 0 code smells.

Security

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

RSEM code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

RSEM is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

RSEM releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 1168 lines of code, 59 functions and 10 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

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RSEM Key Features

No Key Features are available at this moment for RSEM.

RSEM Examples and Code Snippets

No Code Snippets are available at this moment for RSEM.

Community Discussions

Trending Discussions on RSEM

Snakemake - How to set conda environment path

Information on XXX.cnt obtained by an RSEM analysis

Rule-specific wildcards in Snakemake

How do I extract rows from a data frame by identifying a character string in a single column?

QUESTION

Snakemake - How to set conda environment path

Asked 2020-Dec-15 at 08:18

In Snakemake, conda environments can be easily set up by defining rules as such conda: "envs/my_environment.yaml". This way, YAML files specify which packages to install prior to running the pipeline.

Some software requires a path to third-party-software, to execute specific commands.

An example of this is when generating a reference index with RSEM (example from GitHub page DeweyLab - RSEM):

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ANSWER

Answered 2020-Dec-15 at 06:34

There are two ways that I've dealt with this.

1: Let Conda Handle PATH

That specific option (--star-path) only needs to be specified if STAR is not on PATH. However, if STAR is included in your YAML for this rule, then Conda will place it on PATH as part of the environment activation, and so that option won't be needed. Same goes for --bowtie-path. Hence, for such a rule the YAML might be something like:

Source https://stackoverflow.com/questions/65290120

QUESTION

Information on XXX.cnt obtained by an RSEM analysis

Asked 2020-Sep-04 at 06:53

I obtained a "XXX.cnt" in a newly created "XXX.stat" directory after an RSEM-1.3.3 analysis.

Shown below is the content of the XXX.cnt.

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ANSWER

Answered 2020-Sep-04 at 06:53

The format and meanings of each field are described in "cnt_file_description.txt" under RSEM directory.

http://deweylab.github.io/RSEM/rsem-calculate-expression.html#OUTPUT

https://github.com/bli25broad/RSEM_tutorial

Here is the transcript.

Source https://stackoverflow.com/questions/63697139

QUESTION

Rule-specific wildcards in Snakemake

Asked 2020-Aug-27 at 07:22

I often find when adding rules to my workflow that I need to split large jobs up into batches. This means that my input/output files will branch out across temporary sets of batches for some rules before consolidating again into one input file for a later rule. For example:

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ANSWER

Answered 2020-Aug-27 at 07:22

I hope I understood your problem correctly, if not, feel free to correct me:

So, you want to call the rule blast for every "blast_input_{X}.fasta"? Then, the batch wildcard would need to be carried over into the output.

Source https://stackoverflow.com/questions/63609758

QUESTION

How do I extract rows from a data frame by identifying a character string in a single column?

Asked 2020-Jul-30 at 21:05

I have a data frame from TCGAbiolinks and need to narrow it down to just unnormalized data. I tried writing some sort of for loop that will return the rows where the tags variable in subset.gbmexp includes "unnormalized" but can't seem to get the code right. Something along the lines of:

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ANSWER

Answered 2020-Jul-30 at 21:05

Assuming you want to select rows 1, 2, 3 and 6, which contain the character string "unnormalized" in the tags column, you could do:

Source https://stackoverflow.com/questions/63180531

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

Vulnerabilities

No vulnerabilities reported

Install RSEM

To compile pRSEM, type. Note that you need to first compile RSEM before compiling pRSEM. Currently, pRSEM has only been tested on Linux.

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 .

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