2737 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
...proteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic...2581 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), an...893 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...p; make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam #...nimap2 -d MT-human.mmi test/MT-human.fa ./minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam #...2189 days ago
regioneR: an R package for the management and comparison of genomic regions
...rs a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework. With it, it's poss...2015 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can p...1999 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
...sequence identifier. By default, the field separator is the character "|" but custom delimiters can be defined. Examples of trees to test UPhO are provided in the TestData folder.1981 days ago
SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the...1646 days ago
mutatrix: a population genome simulator which generates simulated genomes.
genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms More at https://github.com/ekg/mutatrix ./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta1603 days ago
1426 days ago