Focused crawls are collections of frequently-updated webcrawl data from narrow (as opposed to broad or wide) web crawls, often focused on a single domain or subdomain.
Humbug is a Mutation Testing framework for PHP to measure the real effectiveness of your test suites and assist in their improvement. It eats Code Coverage for breakfast.
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
An R wrapper for SigProfilerExtractor that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
SigProfilerTopography allows evaluating the distribution of somatic mutations and/or mutational signatures across the genomic landscape. The tool evaluates nucleosome occupancy, replication strand bias, transcription strand bias, and replication timing. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
WOLAND is a multiplatform tool to analyze point mutation patterns using resequencing data from any organism or cell. It is implemented as a Perl and R tool using as inputs filtered unannotated or annotated SNV lists, combined with its correspondent genome sequences.
Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.
Projects that use mutation testing, based on mutation operators applied at the level of a statement within a method or a function. The mutated program needs to be strongly killed by the designed test cases. At least three different mutation operators should be used.