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EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2182 days agosourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical...
By Jit 1801 days agodeltarho.org - Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the DeltaRho environment. For those familiar with Trellis...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1035 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 100 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Rahul Agarwal 3461 days ago Comments (1)github.com - GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data.It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2390 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...dcGOR
By Martin Jones 3700 days agoan R package for analysing ontologies and protein domain annotationsSVbyEye: R Package to visualize alignments between two or multiple DNA sequences
By LEGE 100 days agogithub.com - R Package to visualize alignments between two or multiple DNA sequences includinga number of functionalities to facilitate processing of alignments in PAF format. SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence...plumber:An R package that converts your existing R code to a web API
By BioJoker 2114 days agohttps://www.rplumber.io/ - plumber allows you to create a REST API by merely decorating your existing R source code with special comments. Take a look at an example. # plumber.R #* Echo back the input #* @param msg The message to echo #* @get /echo function(msg=""){...Platypus – R package for object detection and image segmentation.
By BioStar 1508 days agogithub.com - platypus is an R package for object detection and semantic segmentation. Currently using platypus you can perform: multi-class semantic segmentation using U-Net architecture multi-class object detection...
