معرفی شرکت ها

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

توضیحات

Small RNAseq pipeline for paired-end reads

ویژگی	مقدار
سیستم عامل	OS Independent
نام فایل	XICRA-1.4.5
نام	XICRA
نسخه کتابخانه	1.4.5
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Jose F. Sanchez-Herrero
ایمیل نویسنده	jfbioinformatics@gmail.com
آدرس صفحه اصلی	https://github.com/HCGB-IGTP/XICRA/
آدرس اینترنتی	https://pypi.org/project/XICRA/
مجوز	MIT License

# XICRA: Small RNAseq pipeline for paired-end reads ## Description XICRA is a python pipeline developed in multiple separated modules that it is designed to take paired end fastq reads, trim adapters and low-quality base pairs positions, and merge reads (R1 & R2) that overlap. Using joined reads it describes all major RNA biotypes present in the samples including miRNA and isomiRs, tRNA fragments (tRFs) and piwi associated RNAs (piRNAs). So far, XICRA produces a miRNA analysis at the isomiR level using joined reads, multiple software at the user selection and following a standardization procedure. Results are generated for each sample analyzed and summarized for all samples in a single expression matrix. This information can be processed at the miRNA or isomiR level (single sequence) but also summarizing for each isomiR variant type. This information can be easily accessed using the accompanied R package XICRA.stats. Although the pipeline is designed to take paired-end reads, it also accepts single-end reads. ## Installation XICRA will require python v3.7 and java (we tested in openjdk 14 2020-03-17). The XICRA python pipeline is available in `pip` and also available using `conda`. XICRA depends on multiple third party software that we have listed below. ### Dependencies Python XICRA module will install itself along some python modules dependencies (pandas, multiqc, pybedtools, biopython etc.). But additionally, XICRA depends on third party software that we listed in the following [table](https://github.com/HCGB-IGTP/XICRA/blob/master/XICRA_pip/XICRA/config/software/soft_dependencies.csv). ### Conda environment We encourage you to install XICRA and all dependencies using the `conda` environment we created and following these instructions. To create a new conda environment, install third party software, install XICRA and missing dependencies, do as follows: 1) Get requirements file from XICRA git repo ```sh wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml ``` 2) Create environment named XICRA and install required packages using conda: ```sh conda env create -f environment.yml ``` 3) Activate environment and install XICRA ```sh ## activate conda activate XICRA ## install latest python code pip install XICRA ``` 4) Install missing software: Unfortunately, a couple of executables are not available neither as a `conda` or `pip` packages. These packages are `miraligner`, `sRNAbench` and 'MINTmap'. We have generated a `bash` script to retrieve and include within your `conda environment`. ```sh ## install missing software wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh sh installer.sh ``` To check everything is fine, try executing the `config` module: ```sh XICRA config ``` ## Documentation See a full documentation, user guide and manual in [here](https://readthedocs.org/) ## Example Here we include a brief example on how to use XICRA. First, we create a python environment and will install XICRA and dependencies. See example details shown before. Then, we can test XICRA by using an example of 100 miRNA simulated and provideded within the repository as an example of simulation. ```sh ## run XICRA example ln -s ~/BMC_bioinformatics_paper/simulation/example/reads/ ## prepare reads XICRA prep --input reads/ --output_folder test_XICRA ## join reads XICRA join --input test_XICRA --noTrim ## create miRNA analysis XICRA miRNA --input test_XICRA --software miraligner sRNAbench ## explore results ls test_XICRA/report/ ``` ## Documentation For a full documentation and details visit Read the Docs site [here](https://xicra.readthedocs.io/). See a brief example on how to install and run XICRA [here](https://github.com/HCGB-IGTP/XICRA/tree/master/XICRA_pip#example) ## License MIT License Copyright (c) 2020-2022 HCGB-IGTP See additional details [here](XICRA_pip/LICENSE) Developed and maintained by Jose F. Sanchez-Herrero and Lauro Sumoy at HCGB-IGTP http://www.germanstrias.org/technology-services/genomica-bioinformatica/ ## Citation Sanchez Herrero, J.F., Pluvinet, R., Luna de Haro, A. et al. Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis. BMC Bioinformatics 22, 215 (2021). https://doi.org/10.1186/s12859-021-04128-1 ## Authors Antonio Luna de Haro (v0.1) Jose F Sanchez-Herrero (v1.0)

نیازمندی

مقدار	نام
-	pandas
-	termcolor
-	cutadapt
-	mirtop
-	pysam
-	pybedtools
-	biopython
-	multiqc
-	HCGB
-	future
-	networkx
-	numpy
-	gitdir

نحوه نصب

نصب پکیج whl XICRA-1.4.5:

pip install XICRA-1.4.5.whl

نصب پکیج tar.gz XICRA-1.4.5:

pip install XICRA-1.4.5.tar.gz