EnzymeML

EnzymeML is a free and open standard based XML markup interchange format for enzyme kinetics.

2023.09.05150

scBasset

Sequence-based modeling of single-cell ATAC-seq using convolutional neural networks.

2023.03.12120

Omnipose

Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways described in our paper. It works for both 2D and 3D images and on any imaging modality or cell shape, so long as you train it on representative images.

2023.03.12120

Light-Seq

Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.

2023.03.12120

AlphaFill

AlphaFill is an algorithm based on sequence and structure similarity that 鈥渢ransplants鈥?missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.

2023.03.12120

MISpheroID

A knowledgebase and transparency tool for minimum information in spheroid identity.

2022.06.02120

LiftPose3D

Deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals.

2022.06.02120

SAVER-X

Data denoising with transfer learning in single-cell transcriptomics

2022.01.19130

SCITO

SCITO-seq: single-cell combinatorial indexed cytometry sequencing

2022.01.19120

CloudReg

CloudReg: automatic terabyte-scale cross-modal brain volume registration

2022.01.19120

Martini 3

Martini 3: a coarse-grained force field with an eye for atomic detail

2022.01.19130

scHOT

Investigating higher-order interactions in single-cell data with scHOT

2022.01.19120

VesSAP

Machine learning analysis of whole mouse brain vasculature

2022.01.19130

cardelino

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

2022.01.19120

TooManyCells

TooManyCells identifies and visualizes relationships of single-cell clades

2022.01.19140

nnU-Net

nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation

2022.01.19140

click-ExM

Click-ExM enables expansion microscopy for all biomolecules

2022.01.19130

diaPASEF

diaPASEF: parallel accumulation?€?serial fragmentation combined with data-independent acquisition

2022.01.19130

PhEMD

Uncovering axes of variation among single-cell cancer specimens

2022.01.19130

wtdbg2

Fast and accurate long-read assembly with wtdbg2

2022.01.19120

TYGRESS

In situ structure determination at nanometer resolution using TYGRESS

2022.01.19130

CLIJ

CLIJ: GPU-accelerated image processing for everyone

2022.01.19140

DIA-NN

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

2022.01.19140

cryoID

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

2022.01.19140

VarID

Revealing dynamics of gene expression variability in cell state space

2022.01.19130

ImJoy

ImJoy: an open-source computational platform for the deep learning era

2022.01.19130

FreeHi-C

FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation

2022.01.19130

Deep-Z

Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning

2022.01.19130

Harmony-R

Fast, sensitive and accurate integration of single-cell data with Harmony

2022.01.19211

RNAEditingIndexer

Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity

2022.01.19160

Warp

Real-time cryo-electron microscopy data preprocessing with Warp

2022.01.19120

Topaz

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

2022.01.19140

mesoSPIM initiative

The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue

2022.01.19130

u-shape3D

Robust and automated detection of subcellular morphological motifs in 3D microscopy images

2022.01.19130

CellAssign

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

2022.01.19120

BindSpace

BindSpace decodes transcription factor binding signals by large-scale sequence embedding

2022.01.19120

Glyco-DIA

Glyco-DIA: a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries

2022.01.19120

FLAM-seq analysis pipeline

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control

2022.01.19130

BigStitcher

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples

2022.01.19130

Emap2sec

Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning

2022.01.19120