137 Open source projects that are alternatives of or similar to velodyn

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Next-Gen Sequencing tools from the Horvath Lab

Single cell analysis in the browser

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

Porting DESeq2 and DEXSeq into python via rpy2

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

RNA-seq analysis pipeline for detection gene-fusions

sssMOR - Sparse State-Space and Model Order Reduction Toolbox

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

Open-source, graph-based Python code generator and analysis toolbox for dynamical systems (pre-implemented and custom models). Most pre-implemented models belong to the family of neural population models.

R package for statistical inference using partially observed Markov processes

Latent Differential Equations models in Julia.

A multi-body simulation software

Version 2.1.0 released

No description or website provided.

mgatk: mitochondrial genome analysis toolkit

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

Streamlining SLAM-seq analysis with ultra-high sensitivity

Multiome GRN inference.

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

Feature extraction algorithm for genomic data

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

Reference mapping for single-cell genomics

🐍 Snakefiles for common RNA-seq data analysis workflows.

Manuscript for functional prediction of transcriptomic “dark matter” across species

spatial transcriptome, single cell

Toolkit for Single-Cell Velocity

Summer school course materials collection

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Reference-based transcript discovery from long RNA read

egtplot: A python package for 3-Strategy Evolutionary Games

A pipeline for the computational evaluation of RNA-Seq data

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Source code for 'Dynamical Systems with Applications Using Python' by Stephen Lynch

Methods for detecting doublets in single-cell sequencing data

Inference of switch-like differential expression along single-cell trajectories

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

The FactorGraph package provides the set of different functions to perform inference over the factor graph with continuous or discrete random variables using the belief propagation algorithm.

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

Simple implementations of chaotic maps in Processing

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

R API and htmlwidget for Vitessce

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Papers with code for single cell related papers

FEELnc : FlExible Extraction of LncRNA

RaPId (a recursive acronym for "Rapid Parameter Identification") utilizes different optimization and simulation technologies to provide a framework for model validation and calibration of any kind of dynamical systems, but specifically catered to power systems.

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

🚦 Run Picard on BAM files and collate 90 metrics into one file.