This package provides a method to sample cells from single-cell data. It also generates an aggregate profile on a pruned K-Nearest Neighbor graph. This approach leads to an improved gene expression profile for quantifying gene regulations.

Pegasusio is a Python package for reading or writing single-cell genomics data.

This package provides R miscellaneous utilities for basic data manipulation, debugging, visualization, lsf management, and common mskilab tasks.

DNA Features Viewer is a Python library to visualize DNA features, e.g. from GenBank or Gff files, or Biopython SeqRecords.

RAxML is a tool for phylogenetic analysis and post-analysis of large phylogenies.

MAFFT offers a range of multiple alignment methods for nucleotide and protein sequences. For instance, it offers L-INS-i (accurate; for alignment of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 sequences).

MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for unassembled metagenomic reads, but is mainly designed for full genomes and assembled metagenomic sequence.

This package provides utility functions and imports for Giotto Suite.

This package provides a VCF parser for Python.

Chromap is a fast method for aligning and preprocessing high throughput chromatin profiles. Typical use cases include:

• trimming sequencing adapters, mapping bulk ATAC-seq or ChIP-seq genomic reads to the human genome and removing duplicates;

• trimming sequencing adapters, mapping single cell ATAC-seq genomic reads to the human genome, correcting barcodes, removing duplicates and performing Tn5 shift;

• split alignment of Hi-C reads against a reference genome.

Bio::Kseq provides ruby bindings to the kseq.h FASTA and FASTQ parsing code. It provides a fast iterator over sequences and their quality scores.

This package builds on Seurat's Doheatmap function code to produce a heatmap from a Seurat object with multiple annotation bars.

This package provides a tool for creating alignment plots from bam files.

This package provides a GFF/GTF file parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

Bloom-filter-based error correction solution for high-throughput sequencing reads (BLESS) uses a single minimum-sized bloom filter is a correction tool for genomic reads produced by Next-generation sequencing (NGS). BLESS produces accurate correction results with much less memory compared with previous solutions and is also able to tolerate a higher false-positive rate. BLESS can extend reads like DNA assemblers to correct errors at the end of reads.

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome.

Cell2cell is a Python library for cell communication analysis. This is a method to calculate, visualize and analyze communication between cell types. Cell2cell is suitable for single-cell RNA sequencing (scRNA-seq) data.

Deacon filters DNA sequences in FASTA/Q files and streams using SIMD-accelerated minimizer comparison with query sequence(s), emitting either matching sequences (search mode), or sequences without matches (deplete mode). Sequences match when they share enough distinct minimizers with the indexed query to exceed chosen absolute and relative thresholds. Query size has little impact on filtering speed, enabling ultrafast search and depletion with gene-, genome- and pangenome-scale queries using a laptop.

t-Stochastic Neighborhood Embedding (t-SNE) is a method for dimensionality reduction and visualization of high dimensional datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to approximate the gradient at each iteration of gradient descent. This implementation differs in these ways:

• Instead of approximating the N-body simulation using Barnes-Hut, we interpolate onto an equispaced grid and use FFT to perform the convolution.

• Instead of computing nearest neighbors using vantage-point trees, we approximate nearest neighbors using the Annoy library. The neighbor lookups are multithreaded to take advantage of machines with multiple cores.

randfold computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

VoltRonStore provides utilities and a resource for installing dependencies of VoltRon package.

The store package provides a number of data store types that are useful for bioinformatic analysis.

This package implements a bioinformatics algorithm for demultiplexing multiplexed single cell datasets. It is built on a statistical model of tag read counts derived from the physical mechanism of tag cross-contamination.

This package provides string parsing functionalities for generating plotnames, filenames and paths.