R-SAP is a user-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. R-SAP accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values.
MemPype is a Python-based pipeline that integrates several tools the prediction of topology and subcellular localization of Eukaryotic membrane proteins.
PGAP (pan-genome analysis pipeline) can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters.
PGAP-X is a microbial comparative genomic analysis platform with graphic interface.
PGAweb is a webserver for bacterial pan-genome analysis. It had integrated our previous published stand-alone tools PGAP, PanGP and PGAP-X into one server and simplifies the analysis of pan-genome.
::DEVELOPER
Beijing Institute of Genomics, Chinese Acadamy of Sciences , Yongbing Zhao
Chen X, Zhang Y, Zhang Z, Zhao Y, Sun C, Yang M, Wang J, Liu Q, Zhang B, Chen M, Yu J, Wu J, Jin Z, Xiao J. PGAweb: A Web Server for Bacterial Pan-Genome Analysis.
Front Microbiol. 2018 Aug 21;9:1910. doi: 10.3389/fmicb.2018.01910. PMID: 30186253; PMCID: PMC6110895.
Zhao Y, Sun C, Zhao D, Zhang Y, You Y, Jia X, Yang J, Wang L, Wang J, Fu H, Kang Y, Chen F, Yu J, Wu J, Xiao J. PGAP-X: extension on pan-genome analysis pipeline.
BMC Genomics. 2018 Jan 19;19(Suppl 1):36. doi: 10.1186/s12864-017-4337-7. PMID: 29363431; PMCID: PMC5780747.
Bioinformatics. 2012 Feb 1;28(3):416-8. doi: 10.1093/bioinformatics/btr655. Epub 2011 Nov 29. PGAP: pan-genomes analysis pipeline.
Zhao Y1, Wu J, Yang J, Sun S, Xiao J, Yu J.
XAEM implements the design matrix and alternating EM (AEM) algorithm, which allows a fast and accurate quantification of isoform expression using multiple samples. In differential expression (DE) analysis of single-cell data XAEM substantially outperforms other methods.
The Taiji software is an integrative multi-omics data analysis framework. It can be used as a standalone pipeline to analyze ATAC-seq, RNA-seq, single cell ATAC-seq or Drop-seq data. However, the uniqueness and the power of Taiji really lie in its ability to integrate diverse datasets and use these information in a clever way to construct regulatory network and identify candidate driver genes.
piPipes is a coordinated set of pipelines to analyze piRNA (PIWI-interacting RNAs) and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq.
CG-Pipeline is an analytical pipeline for the analysis of prokaryotic genome sequences. Includes genome assembly, gene prediction and fucntional annotation.
Kislyuk, A. O., L. S. Katz, S. Agrawal, M. S. Hagen, A. B. Conley, P. Jayaraman, V. Nelakuditi, J. C. Humphrey, S. A. Sammons, D. Govil, R. D. Mair, K. M. Tatti, M. L. Tondella, B. H. Harcourt, L. W. Mayer, and I. K. Jordan. 2010. A computational genomics pipeline for prokaryotic sequencing projects.
Bioinformatics 26:1819-26.
