| Updated | Application
| 22 Sep 2023 | cellranger updated to version 7.2.0 | Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. 22 Sep 2023 | dotnet updated to version 6.0.22 | .NET Core Runtime 22 Sep 2023 | fragpipe updated to version 20.0 | FragPipe is a Java Graphical User Interface (GUI) and CLI workflow tool for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger. 22 Sep 2023 | msfragger updated to version 3.8 | An ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. 22 Sep 2023 | ionquant updated to version 1.9.8 | IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe (recommended option), but can also be run as a command-line tool. 21 Sep 2023 | epic2 updated to version 0.0.52 | epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use. 20 Sep 2023 | CTF updated to version 6.1 | The CTF MEG software has two main roles: - Provide a human-machine interface to the CTF MEG elec- tronics to collect MEG and/or EEG data. - Provide a tool for reviewing and (to a limited extent) ana- lyzing the MEG and/or EEG data acquired by the CTF MEG system. 18 Sep 2023 | xcp_d updated to version 0.5.0 | xcp_d is a postprocessing and noise regression pipeline for fMRI datasets (can use output from fmriprep and nibabies). 17 Sep 2023 | esm updated to version 2.0.0-74-g2b36991 | Code and pre-trained weights for Transformer protein language models from the Meta Fundamental AI Research Protein Team (FAIR) 13 Sep 2023 | nextflow updated to version 23.04.3 | Data-driven computational pipelines 13 Sep 2023 | AlphaPulldown updated to version 0.30.7 | AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command-line interface, a variety of confidence scores and a graphical analysis tool. 12 Sep 2023 | picard updated to version 3.1.0 | Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported. 12 Sep 2023 | fcs updated to version 0.4.0 | FCS is a toolset to remove contaminant sequences from a genome assembly. 12 Sep 2023 | medaka updated to version 1.9.1 | medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. 11 Sep 2023 | verkko updated to version 1.4.1 | Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads. 11 Sep 2023 | bonito updated to version 0.7.2 | A PyTorch Basecaller for Oxford Nanopore Reads 11 Sep 2023 | dxda updated to version 0.6.0 | CLI tool to manage the download of large quantities of files from DNAnexus 11 Sep 2023 | rust updated to version 1.72.0 | A language empowering everyone to build reliable and efficient software. 11 Sep 2023 | snakemake updated to version 7.32.3 | Snakemake aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style. It is well suited for bioinformatic workflows. 11 Sep 2023 | quarto updated to version 1.3.450 | Quarto is an open-source scientific and technical publishing system built on Pandoc 11 Sep 2023 | golang updated to version 1.21.1 | The Go programming language 11 Sep 2023 | gutSMASH updated to version 0-20210610 | gutSMASH is a tool that has been developed to systematically evaluate the metabolic potential of anaerobic bacteria in the gut by predicting both known and novel anaerobic metabolic gene clusters from the gut microbiome. 7 Sep 2023 | checkm2 updated to version 1.0.2 | Rapid assessment of genome bin quality using machine learning. 6 Sep 2023 | pdb2pqr updated to version 3.6.1 | Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling 6 Sep 2023 | dorado updated to version 0.3.4 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 6 Sep 2023 | guppy updated to version 6.5.7 | Local accelerated basecalling for Nanopore data 6 Sep 2023 | parallel updated to version 20230822 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 6 Sep 2023 | netOglyc updated to version 4.0 | NetOglyc produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. 31 Aug 2023 | sequencetubemap updated to version 2023.8 | A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. 31 Aug 2023 | DeepCell-tf updated to version 0.12.6 | The DeepCell-tf library allows users to apply pre-existing models to imaging data as well as to develop new deep learning models for single-cell analysis. The library specializes in models for cell segmentation (whole-cell and nuclear) in 2D and 3D images as well as cell tracking in 2D time-lapse datasets. The models are applicable to data ranging from multiplexed images of tissues to dynamic live-cell imaging movies. 31 Aug 2023 | ROBOT updated to version 1.9.4 | ROBOT is a command-line tool and library for automating ontology development tasks, with a focus on Open Biological and Biomedical Ontologies (OBO). It can be used as a command-line tool or as a library for any language on the Java Virtual Machine. 30 Aug 2023 | cytotrace updated to version 0.3.3 | CytoTRACE (Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression) is a computational method that predicts the differentiation state of cells from single-cell RNA-sequencing data. CytoTRACE leverages a simple, yet robust, determinant of developmental potential—the number of detectably expressed genes per cell, or gene counts. We have validated CytoTRACE on ~150K single-cell transcriptomes spanning 315 cell phenotypes, 52 lineages, 14 tissue types, 9 scRNA-seq platforms, and 5 species. 30 Aug 2023 | plastimatch updated to version 1.9.3 | Application for registration of medical images such as X-rays, CT, MRI and PET 28 Aug 2023 | AFNI updated to version current-py3 | AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. 24 Aug 2023 | paraview updated to version 5.11.1 | ParaView is an open-source, multi-platform data analysis and visualization application. 24 Aug 2023 | CIRCLE-seq updated to version 1.1 | CIRCLE-seq is a tool ifor analysis of circularization for in vitro reporting of cleavage effects by sequencing. It is a highly sensitive, sequencing-efficient in vitro screening strategy that outperforms existing cell-based or biochemical approaches for identifying CRIScrisPR–Cas9 genome-wide off-target mutations. It can be practiced using widely accessible next-generation sequencing technology and does not require reference genome sequences. Importantly, CIRCLEcircle-seq can be used to identify off-target mutations associated with cell-type-specific single-nucleotide polymorphisms, demonstrating the feasibility and importance of generating personalized specificity profiles. 22 Aug 2023 | Matlab updated to version 2023a | MATLAB is an interactive software package for scientific and engineering numeric computation. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an environment where problems and solutions are expressed just as they are written mathematically. 18 Aug 2023 | napari updated to version 0.4.18 | napari is an image viewer.Can be used to annotate images. 16 Aug 2023 | focus updated to version 0.802 | FOCUS (Fine-mapping Of CaUsal gene Sets) is software to fine-map transcriptome-wide association study statistics at genomic risk regions. The software takes as input summary GWAS data along with eQTL weights and outputs a credible set of genes to explain observed genomic risk. 15 Aug 2023 | fmriprep updated to version 23.1.4 | A Robust Preprocessing Pipeline for fMRI Data 15 Aug 2023 | mriqc updated to version 23.1.0 | MRIQC is an MRI quality control tool 11 Aug 2023 | shasta updated to version 0.11.1 | De novo assembly from Oxford Nanopore reads 10 Aug 2023 | Mathematica updated to version 13.3.0 | Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language. 8 Aug 2023 | tomotwin updated to version 0.5.0 | TomoTwin - a deep metric learning based particle picking procedure for cryo-ET 3 Aug 2023 | megit updated to version 0.4.0 | Minimal Eclipe GIT. A graphical front end for git based off the eclipse IDE. 3 Aug 2023 | flanker updated to version 0.1.5 | Gene-flank analysis tool 2 Aug 2023 | fithic updated to version 2.0.8 | Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C. 1 Aug 2023 | Perl updated to version 5.38 | Perl is a highly capable, feature-rich programming language with over 30 years of development. 1 Aug 2023 | htseq updated to version 2.0.4 | HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. 1 Aug 2023 | nested updated to version 2.0.0 | nested (now also called TE-greedy) is software to analyze nested LTR transposable elements in DNA sequences, such as reference genomes. 28 Jul 2023 | pvactools updated to version 4.0.1 | pVACtools is a cancer immunotherapy suite consisting of pVACseq, pVACfuse, pVACvector 28 Jul 2023 | PartekFlow updated to version 10.0.23.0720 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 28 Jul 2023 | Genome Browser updated to version 451 | The Genome Browser Mirror Fragments is a mirror of the UCSC Genome Browser. The URL is https://hpcnihapps.cit.nih.gov/genome. Users can also access the MySQL databases, supporting files directly, and a huge number of associated executables. 27 Jul 2023 | chap updated to version 0.9.1 | CHAP is a tool for the functional annotation of ion channel structures 27 Jul 2023 | model-angelo updated to version 1.0.1 | ModelAngelo is an automatic atomic model building program for cryo-EM maps. 27 Jul 2023 | fastq_demux updated to version 20230713 | fastq_demux is a simple program to demultiplex a FASTQ file or a pair of FASTQ files based on the barcodes present in the FASTQ headers. 27 Jul 2023 | libfreetype updated to version 2.13.1 | FreeType is a freely available software library to render fonts. 27 Jul 2023 | Rosetta updated to version 2023.26 | The Rosetta++ software suite can perform de novo protein structure predictions, identify low free energy sequences for target protein backbones, predict the structure of a protein-protein complex from the individual structures of the monomer components, incorporate NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction, and more... 26 Jul 2023 | fusioninspector updated to version 2.6.0 | In silico Validation of Fusion Transcript Predictions 26 Jul 2023 | mosaics updated to version 1.0.0 | A collection of tools for characterizing membrane structure and dynamics within simulated trajectories of molecular systems. 26 Jul 2023 | xtail updated to version 1.1.5 | Xtail is an analysis pipeline tailored for ribosome profiling data that comprehensively and accurately identifies differentially translated genes in pairwise comparisons. Applied on simulated and real datasets, Xtail exhibits high sensitivity with minimal false-positive rates, outperforming existing methods in the accuracy of quantifying differential translations. 26 Jul 2023 | rdfind updated to version 1.6.0 | rdfind is a program that finds duplicate files. It is useful for compressing backup directories or just finding duplicate files. It compares files based on their content, NOT on their file names. After typing module load rdfind, type man rdfind for more information. 26 Jul 2023 | MySQL updated to version 8.0.34 | MySQL is an open-source relational database management system. 26 Jul 2023 | graphmap updated to version 0.5.2 | GraphMap is a highly sensitive and accurate mapper for long, error-prone reads. It offers a number of valuable features, such as mapping position agnostic to alignment parameters, high sensitivity and precision, handling circular genomes, meaningful mapping quality, various alignment strategies, and more. 26 Jul 2023 | boost updated to version 1.82 | Boost provides free peer-reviewed portable C++ source libraries. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. 26 Jul 2023 | picrust updated to version 2.5.2 | PICRUSt is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. 26 Jul 2023 | deepmedic updated to version 0.8.4 | This project aims to offer easy access to Deep Learning for segmentation of structures of interest in biomedical 3D scans. It is a system that allows the easy creation of a 3D Convolutional Neural Network, which can be trained to detect and segment structures if corresponding ground truth labels are provided for training. The system processes NIFTI images, making its use straightforward for many biomedical tasks. 26 Jul 2023 | CCP4 updated to version 8.0.013 | CCP4 is a suite of programs for protein crystallography and structural biology. 25 Jul 2023 | MINTIE updated to version 0.4.2 | MINTIE is a tool for identifying novel, rare transcriptional variants in cancer RNA-seq data. MINTIE detects gene fusions, transcribed structural variants, novel splice variants and complex variants, and annotates all novel transcriptional variants. 25 Jul 2023 | EMAN2 updated to version 2.99 | EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. 25 Jul 2023 | zstd updated to version 1.5.5 | Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios. 25 Jul 2023 | inkscape updated to version 1.3 | Inkscape is a Free and open source vector graphics editor 25 Jul 2023 | azure_cli updated to version 2.50.0 | 25 Jul 2023 | talon updated to version 5.0-60-g2e538a8 | TALON is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. 24 Jul 2023 | pb-cpg-tools updated to version 2.3.1 | Tools for analyzing CpG/5mC data from PacBio HiFi reads aligned to a reference genome 23 Jul 2023 | vcfpy updated to version 0.13.6 | Python library for handling the variant call format. Differs from pyvcf in that it has the ability to modify per-sample genotype information. 23 Jul 2023 | nodejs updated to version 18.17.0 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 23 Jul 2023 | rmblast updated to version 2.14.0 | RMBlast is a RepeatMasker-compatible version of the standard NCBI blastn program. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. 23 Jul 2023 | k8 updated to version 0.2.5 | javascript shell based on v8, but with fasta/fastq parser and the ability to open files on the filesystem 21 Jul 2023 | VEP updated to version 110 | VEP (Variant Effect Predictor) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. 20 Jul 2023 | visidata updated to version 2.11.1 | VisiData is an interactive multitool for tabular data 19 Jul 2023 | DNAnexus updated to version 0.352.1 | DNAnexus is a cloud-based commercial solution for next-generation sequence analysis and visualization. It has a command-line interface (CLI) which can be used to log in to the DNAnexus platform, upload and navigate data, and launch analyses. 13 Jul 2023 | interproscan updated to version 5.63-95.0 | InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium. |