This package provides a collection of useful functions for working with DNA methylation micro-array data.

A streamgraph is a type of stacked area chart. It represents the evolution of a numeric variable for several groups. Areas are usually displayed around a central axis, and edges are rounded to give a flowing shape. This package provides an htmlwidget for building streamgraph visualizations.

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.

PiGx is a collection of genomics pipelines. It includes the following pipelines:

• PiGx BSseq for raw fastq read data of bisulfite experiments

• PiGx RNAseq for RNAseq samples

• PiGx scRNAseq for single cell dropseq analysis

• PiGx ChIPseq for reads from ChIPseq experiments

All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Its features include:

1. Simple, easy to use pipeline to screen genes in Genome-wide CRISPR-Cas9 Knockout experiments;

2. High sensitivity and low false discovery rate;

3. Fully utilize the screening data by performing both positive and negative screening in one dataset;

4. Provide statistical evaluation in genes, sgRNAs and pathways;

5. Require as few as 2 samples;

6. Identify cell-type specific targets;

7. A set of visualization features that generate publication standard figures.

This package provides a Python package for reading raw fcs files

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.

PAIRADISE is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.

This is an R package providing additional capabilities and speed for GenomicRanges operations.

This package provides several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable called bam.

Skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

Aragorn identifies transfer RNA, mitochondrial RNA and transfer-messenger RNA from nucleotide sequences, based on homology to known tRNA consensus sequences and RNA structure. It also outputs the secondary structure of the predicted RNA.

This package provides a simple web interface for the RNA-centric annotation system (RCAS).

This package is a set of R functions for generating precise figures. This tool helps you to create clean markdown reports about what you just discovered with your analysis script.

Bowtie is a fast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees.

This is a set of R functions that allows you to generate precise figures. This tool will create clean markdown reports about what you just discovered.

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. Its main features are:

• Bisulfite mapping and methylation calling in one single step

• Supports single-end and paired-end read alignments

• Supports ungapped and gapped alignments

• Alignment seed length, number of mismatches etc are adjustable

• Output discriminates between cytosine methylation in CpG, CHG and CHH context

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig) sequences, and reconstructing germline sequences.

The subread package contains the following tools: subread aligner, a general-purpose read aligner; subjunc aligner: detecting exon-exon junctions and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic features; exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

python-cwlformat is a specification and a reference implementation for a very opinionated CWL code formatter. It outputs CWL in a standardized YAML format.

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.

Bíogo is a bioinformatics library for the Go language.