SBGrid Consortium homepage

a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.

a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).

Find rearrangements in "long" DNA reads relative to a genome sequence.

RNA-seq data normalization in Python.

a fast, low-memory assembler designed for long and accurate metagenomic reads, such as those produced by PacBio HiFi and Nanopore sequencing.

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

a GPU-enabled QTL mapper, achieving ~200-300 fold faster cis- and trans-QTL mapping compared to CPU-based implementations.

Visium Spatial Software Suite for analyzing and visualizing spatial gene and protein expression data

an assembly pipeline for bacterial genomes.

a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.