This is a drop-in replacement for the IlluminaHumanMethylationEPIC package. It utilizes a Manifest based on 1.0B5 annotation. As of version 0.3.0, the IlluminaHumanMethylationEPIC package still employs the 1.0B2 annotation manifest. A corresponding annotation package, IlluminaHumanMethylationEPICanno.ilm10b5.hg38, is available to ensure proper annotation. The decision to maintain the same name is due to complications in downstream processing caused by array name lookup in certain preprocessing options.

This program compares version strings. It intends to be a replacement for strverscmp.

python-cwl-upgrader is a standalone upgrader for CWL documents from version draft-3, v1.0, and v1.1 to v1.2.

Fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool has multi-threading support to afford high performance.

Fxtract extracts sequences from a protein or nucleotide fastx (FASTA or FASTQ) file given a subsequence. It uses a simple substring search for basic tasks but can change to using POSIX regular expressions, PCRE, hash lookups or multi-pattern searching as required. By default fxtract looks in the sequence of each record but can also be told to look in the header, comment or quality sections.

This is an R package for pre-processing of flow and mass cytometry data. This package includes panel editing or renaming for FCS files, bead-based normalization and debarcoding.

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

R-scape discovers RNA secondary structure consensus elements. These elements include riboswitches and ribozymes. It utilizes probabilistic modeling of sequence alignments, explicitly considering folding dependencies. The tool enables the de novo search for new structural elements and facilitates comparative analysis of known RNA families.

PiGx BSseq is a data processing pipeline for raw fastq read data of bisulfite experiments; it produces reports on aggregate methylation and coverage and can be used to produce information on differential methylation and segmentation.

BWA-PSSM is a probabilistic short genomic sequence read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it is also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.

Discrover is a motif discovery method to find binding sites of nucleic acid binding proteins.

The NCBI-VDB library implements a highly compressed columnar data warehousing engine that is most often used to store genetic information. Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.

This is the reference implementation of the CWL standards. The CWL open standards are for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. The cwltool is intended to be feature complete and to provide comprehensive validation of CWL files as well as provide other tools related to working with CWL descriptions.

F-Seq is a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome Browser.

This package provides a toolbox to process, analyze and visualize spatial single-cell expression data.

This package provides an automated pipeline for spatial mapping of unique transcripts.

This package provides a new batch effect correction method based on Projection to Latent Structures Discriminant Analysis named “PLSDA-batch” to correct data prior to any downstream analysis. PLSDA-batch estimates latent components related to treatment and batch effects to remove batch variation. The method is multivariate, non-parametric and performs dimension reduction. Combined with centered log ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far.

LAMMPS is a classical molecular dynamics simulator designed to run efficiently on parallel computers. LAMMPS has potentials for solid-state materials (metals, semiconductors), soft matter (biomolecules, polymers), and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

ScVelo is a scalable toolkit for RNA velocity analysis in single cells. RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics. scVelo generalizes the concept of RNA velocity by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.

Circe is a Python package for inferring co-accessibility networks from single-cell ATAC-seq data, using skggm for the graphical lasso and python-scanpy for data processing.

This is a set of functions for processing raw scDam&T-seq data. scDam&T-seq is a method to simultaneously measure protein-DNA interactions and transcription from single cells (Rooijers et al., 2019). It combines a DamID-based method to measure protein-DNA interactions and an adaptation of CEL-Seq to measure transcription. The starting point of the workflow is raw sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq counts.

Megahit is a fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

This package provides an accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies.

This package provides Python bindings to the libBigWig library for accessing bigWig files.