This package is used to apply filtering on raw VCF calls generated using CaVEMan.

This module provides code coverage metrics for Perl. Code coverage metrics describe how thoroughly tests exercise code. By using Devel::Cover you can discover areas of code not exercised by your tests and determine which tests to create to increase coverage.

This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

This package provides the reference implementation of CGP workflow for CaVEMan SNV analysis.

The io_lib from the Staden package is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. It supports various DNA sequence read formats, in particular SCF, ABI, ALF, CTF, ZTR, SFF and SRF.

This package provides a tool to download or view data in the cloud environments of ICGC.

This package provides a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). It uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. It further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

CMAPLE is a C++ reimplementation of MAPLE - a novel likelihood-based phylogenetic inference method for pandemic-scale epidemiological genomic data.

diemPy is a computational tool designed to polarize genomic data for hybrid zone analysis. The package implements an expectation-maximization (EM) algorithm to determine the optimal polarization of genetic markers, enabling researchers to identify and analyze patterns of introgression and hybridization in genomic datasets.

Framework for analyzing low-depth NGS data in heterogeneous/structured populations using PCA. Population structure is inferred by estimating individual allele frequencies in an iterative approach using a truncated SVD model. The covariance matrix is estimated using the estimated individual allele frequencies as prior information for the unobserved genotypes in low-depth NGS data.

The estimated individual allele frequencies can further be used to account for population structure in other probabilistic methods. pcangsd can be used for the following analyses:

• Covariance matrix

• Admixture estimation

• Inbreeding coefficients (both per-sample and per-site)

• HWE test

• Genome-wide selection scans

• Genotype calling

• Estimate NJ tree of samples

Mellon is a non-parametric cell-state density estimator based on a nearest-neighbors-distance distribution. It uses a sparse gaussian process to produce a differntiable density function that can be evaluated out of sample.

This package provides procedures to calculate statistics for Oxford Nanopore sequencing data and alignments.

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data such as:

• Recombination model probability distribution

• Hypermutation model

• Best candidates recombination scenarios

• Generation probabilities of sequences (even hypermutated)

Its heavily object oriented and modular style was designed to ensure long term support and evolvability for new tasks in assessing TCR and BCR receptors features using modern parallel architectures.

This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.

Build contrasts for models defined with formulaic.

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). It achieves this without requiring subsampling or aggregation.