gffcompare is a tool that can:

1. compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie);

2. collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples);

3. classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format).

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.

ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and HCV) that experience substantial biological insertions and deletions.

Salmon is a program to produce highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of lightweight alignments (accurate but fast-to-compute proxies for traditional read alignments) and massively-parallel stochastic collapsed variational inference.

This package stores motif collections as lists of position frequency matrix (PWMatrixList) objects provided by the TFBSTools package for use in R with packages like motifmatchr or chromVAR.

This package is a library to enable flexible and scalable operations on genomic interval dataframes in Python. Bioframe enables access to a rich set of dataframe operations. Working in Python enables rapid visualization and iteration of genomic analyses. The philosophy underlying bioframe is to enable flexible operations. Instead of creating a function for every possible use-case, we encourage users to compose functions to achieve their goals.

The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.

This package detects naive associations between omics features and metadata in cross-sectional data-sets using non-parametric tests. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests. The generated output can be graphically summarized using the built-in plotting function.

This package implements FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.

BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

This package provides the core libraries.

SlamDunk is a fully automated tool for automated, robust, scalable and reproducible SLAMseq data analysis. Diagnostic plotting features and a MultiQC plugin will make your SLAMseq data ready for immediate QA and interpretation.

This package facilitates the analysis of single-cell RNA-seq UMI matrices. It does this by computing partitions of a cell similarity graph into small homogeneous groups of cells, which are defined as metacells (MCs). The derived MCs are then used for building different representations of the data, allowing matrix or 2D graph visualization forming a basis for analysis of cell types, subtypes, transcriptional gradients,cell-cycle variation, gene modules and their regulatory models and more.

ctxcore is part of the SCENIC suite of tools. It provides core functions for pycisTarget and SCENIC.

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.

An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.

An interval map structure that is optimized for low memory (each interval is represented by about 3 words + whatever the cargo is) and has semantics that are appropriate for genomic intervals (namely, intervals can overlap and queries will return all matches together). It also designed to be used in two phases: a construction phase + query phase).

The loom file format is an efficient format for very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations. Loom also supports sparse graphs. This library makes it easy to work with .loom files for single-cell RNA-seq data.

This package can be used to normalize cytometry samples when a control sample is taken along in each of the batches. This is done by first identifying multiple clusters/cell types, learning the batch effects from the control samples and applying quantile normalization on all markers of interest.

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

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.

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

The ZarrArray package leverages the Rarr package to bring Zarr datasets in R as DelayedArray objects. The main class in the package is the ZarrArray class. A ZarrArray object is an array-like object that represents a Zarr dataset in R. ZarrArray objects are DelayedArray derivatives and therefore support all operations (delayed or block-processed) supported by DelayedArray objects.

This package provides necessary tools for the analysis of the genomic interaction data stored in .cool format. This collection of tools includes operations like compartment, insulation or peak calling.

bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.