:: DESCRIPTION
SCRIP provides a flexible Gamma-Poisson mixture and a Beta-Gamma-Poisson mixture framework to simulate scRNA-seq data.
::DEVELOPER
Fei Qin [aut, cre, cph]
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Qin F, Luo X, Xiao F, Cai G.
SCRIP: an accurate simulator for single-cell RNA sequencing data.
Bioinformatics. 2021 Dec 7:btab824. doi: 10.1093/bioinformatics/btab824. Epub ahead of print. PMID: 34874992.
:: DESCRIPTION
Circall is a novel method for fast and accurate discovery of circular RNAs from paired-end RNA-sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nguyen DT, Trac QT, Nguyen TH, Nguyen HN, Ohad N, Pawitan Y, Vu TN.
Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data.
BMC Bioinformatics. 2021 Oct 13;22(1):495. doi: 10.1186/s12859-021-04418-8. PMID: 34645386; PMCID: PMC8513298.
:: DESCRIPTION
PRADA is a flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion variants, homology scores and fusion frame classification.
::DEVELOPER
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PRADA: pipeline for RNA sequencing data analysis.
Torres-García W, Zheng S, Sivachenko A, Vegesna R, Wang Q, Yao R, Berger MF, Weinstein JN, Getz G, Verhaak RG.
Bioinformatics. 2014 Apr 25.
:: DESCRIPTION
ISOP (ISOform Patterns) is a mixture model o characterize the expression patterns of pairs of isoform from the same genes and determine if isoform-level expression patterns are random or signify biological effects.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Pawitan Y, Rantalainen M.
Isoform-level gene expression patterns in single-cell RNA-sequencing data.
Bioinformatics. 2018 Jul 15;34(14):2392-2400. doi: 10.1093/bioinformatics/bty100. PMID: 29490015; PMCID: PMC6041805.
:: DESCRIPTION
SCmut is a novel and robust statistical method for cell-level somatic mutation detection from single-cell RNA-sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Vu TN, Nguyen HN, Calza S, Kalari KR, Wang L, Pawitan Y.
Cell-level somatic mutation detection from single-cell RNA sequencing.
Bioinformatics. 2019 Nov 1;35(22):4679-4687. doi: 10.1093/bioinformatics/btz288. PMID: 31028395; PMCID: PMC6853710.
:: DESCRIPTION
miRPlant extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC:
miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data.
BMC bioinformatics 2014, 15(1):275.
:: DESCRIPTION
GETUTR provides a landscape of 3′ UTR from RNA-seq data. It has three steps: preprocessing, smoothing and normalization.
:: DEVELOPER
BIG Lab. (BIOINFORMATICS & GENOMICS)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Global Estimation of the 3′ Untranslated Region Landscape Using RNA Sequencing.
Kim M, You BH, Nam JW.
Methods. 2015 Apr 18. pii: S1046-2023(15)00157-7. doi: 10.1016/j.ymeth.2015.04.011.
:: DESCRIPTION
deGPS is a powerful and robust tool for detecting differential expression in RNA-Seq data.
::DEVELOPER
Chen Chu (chuchen.blueblues@gmail.com)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies.
Chu C, Fang Z, Hua X, Yang Y, Chen E, Cowley AW Jr, Liang M, Liu P, Lu Y.
BMC Genomics. 2015 Jun 13;16:455. doi: 10.1186/s12864-015-1676-0.
:: DESCRIPTION
cisASE is a likelihood-based method for ASE detection at multiple levels(SNV,exon and gene). It takes matched DNA sequencing data as reference to reduce artifacts from technical bias and copy number variation to identify ASE due to cis-acting elements, and it works almost as well for dataset without DNA sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
cisASE: A likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data.
Liu Z, Gui T, Wang Z, Li H, Fu Y, Dong X, Li Y.
Bioinformatics. 2016 Jul 13. pii: btw416.
:: DESCRIPTION
NASTIseq is a software package for the identiffcation of cis-Natural Antisense Transcripts (cis-NAT) using strand speciffc RNA-seq data. The method is based on the observation that strand speciffc RNAseq sometimes generate reads from the unexpected strand. We designed a probabilistic model which estimate the strand speciffcity and account for it using a binomial model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Song Li, Louisa Liberman, Neelanjan Mukherjee, Philip N. Benfey, Uwe Ohler. (2013).
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.
Genome Res. 2013 Oct;23(10):1730-9. doi: 10.1101/gr.149310.112.
