Jit
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Alignment-free sequence comparison tools available for next-generation sequencing data analysis
Last updated 2607 days ago by Abhimanyu Singh Comments (1)kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...PGAP-X: Extension on pan-genome analysis pipeline
By Rahul Nayak 2529 days agohttps://pgapx.ybzhao.com/ - PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different...bpRNA: large-scale automated annotation and analysis of RNA secondary structure
By Rahul Nayak 2410 days agogithub.com - bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...netGO: R-Shiny package for network-integrated pathway enrichment analysis
By Jit 1779 days agogithub.com - netGO is an R/Shiny package for network-integrated pathway enrichment analysis.netGO provides user-interactive visualization of enrichment analysis results and related networks. Currently, netGO supports analysis for four species...Breedbase is a comprehensive breeding management and analysis software
By BioStar 1450 days agohttps://breedbase.org/ - Breedbase is a comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping samples in a field, store large amounts of high...kebabs: package provides functionality for kernel based analysis of biological sequences via...
By Rahul Nayak 1029 days agowww.bioinf.jku.at - The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define...Powerful books for learning data analysis with R
By LEGE 213 days agohttps://r-graphics.org/ - R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R...EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer...
By Surabhi Chaudhary 2421 days agobmcgenomics.biomedcentral.com - SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 136 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...MGRA: Breakpoint graphs and ancestral genome reconstructions
By Jit 2711 days ago Comments (1)http://mgra.cblab.org/ - MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes. It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and...
