Software Updates

simpleaf

simpleaf is a rust framework to make using alevin-fry even simpler.

HMMER

is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

simpleaf

simpleaf is a rust framework to make using alevin-fry even simpler.

HMMER

is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

dREG

Detection of Regulatory DNA Sequences using GRO-seq Data.

Predictosaurus

a command-line tool designed for uncertainty-aware haplotype-based genomic variant effect prediction. It provides comprehensive functionality for building variant graphs, processing genomic features, and extracting peptide sequences. The tool integrates various bioinformatics processes to support efficient data analysis and visualization.

vireosnp

Vireo: Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data.

skDER

efficient & high-resolution dereplication of microbial genomes

GMAP

Genomic mapping and alignment program for mRNA and EST sequences.

UniFrac

Fast phylogenetic diversity calculations

ensembl_vep

predicts the functional effects of genomic variants

JupyterLab

a program for the next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.

PyMOL Open Source

open source version of the widely used molecular visualization package developed by Warren DeLano.

Bakta

rapid and standardized annotation of bacterial genomes & plasmids.