This package offers a quick and straight-forward way to explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq.

NGS is a domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously.

ikarus is a stepwise machine learning pipeline that tries to cope with a task of distinguishing tumor cells from normal cells. Leveraging multiple annotated single cell datasets it can be used to define a gene set specific to tumor cells. First, the latter gene set is used to rank cells and then to train a logistic classifier for the robust classification of tumor and normal cells. Finally, sensitivity is increased by propagating the cell labels based on a custom cell-cell network. ikarus is tested on multiple single cell datasets to ascertain that it achieves high sensitivity and specificity in multiple experimental contexts.

Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Importantly, "informative" is decided based on how well a gene's variation agrees with some cell metric---some similarity mapping between cells. Genes which are informative are those whose expression varies in similar way among cells which are nearby in the given metric.

METAL is a tool for meta-analysis genomewide association scans. METAL can combine either test statistics and standard errors or p-values across studies (taking sample size and direction of effect into account). METAL analysis is a convenient alternative to a direct analysis of merged data from multiple studies. It is especially appropriate when data from the individual studies cannot be analyzed together because of differences in ethnicity, phenotype distribution, gender or constraints in sharing of individual level data imposed. Meta-analysis results in little or no loss of efficiency compared to analysis of a combined dataset including data from all individual studies.

The goal of anpan is to consolidate statistical methods for strain analysis. This includes automated filtering of metagenomic functional profiles, testing genetic elements for association with outcomes, phylogenetic association testing, and pathway-level random effects models.

This package provides graphical user interfaces to organize and visualize Nanopore sequencing data.

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.

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.

This package contains gatingTemplates, example fcs files and compensation controls for use in CytoExploreR.

This package provides Python bindings to the UCSC Big Binary (bigWig/bigBed) file library. This provides read-level access to local and remote bigWig and bigBed files but no write capabilitites. The main feature is fast retrieval of range queries into numpy arrays.

This tool detects batch effects in high-dimensional data based on chi^2-test.

This is a package for fast Non-negative Matrix Factorization (NMF) with automatic rank-determination for dimension reduction of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. The output consists of two files: a repeat table file and an alignment file. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected.

This package implements methods to project single-cell RNA-seq data onto a reference atlas, enabling interpretation of unknown cell transcriptomic states in the the context of known, reference states.

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are:

• Import of data from BAM, SAM or FastQ files (any variant);

• Providing a quick overview to tell you in which areas there may be problems;

• Summary graphs and tables to quickly assess your data;

• Export of results to an HTML based permanent report;

• Offline operation to allow automated generation of reports without running the interactive application.

EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018).

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.

This package allows building the hierarchy of domains starting from Hi-C data. Each hierarchical level is identified by a minimum value of physical insulation between neighboring domains.

CD-HIT is a program for clustering and comparing protein or nucleotide sequences. CD-HIT is designed to be fast and handle extremely large databases.

PhenoGraph is a clustering method designed for high-dimensional single-cell data. It works by creating a graph representing phenotypic similarities between cells and then identifying communities in this graph.

MAGIC is an interactive tool to impute missing values in single-cell sequencing data and to restore the structure of the data. It also provides data pre-processing functionality such as dimensionality reduction and gene expression visualization.