Optimus 5-Prime
Optimus 5-Prime is a deep neural network that can predict how variants in human 5' UTR sequences influence ribosome loading.
APARENT
APARENT is a deep neural network that can predict human 3' UTR Alternative Polyadenylation (APA) and the effects of genetic variants on APA. The network was trained on >3.5 million randomized 3' UTR poly-A signals expressed on mini gene reporters in HEK293.
SPLiT-seq
Split-seq is our approach to high-throughput single-cell RNA sequencing. Check out this video to see how it works. You can download a table of the oligos and detailed protocol here:
Optimus 5-Prime is a deep neural network that can predict how variants in human 5' UTR sequences influence ribosome loading.
APARENT
APARENT is a deep neural network that can predict human 3' UTR Alternative Polyadenylation (APA) and the effects of genetic variants on APA. The network was trained on >3.5 million randomized 3' UTR poly-A signals expressed on mini gene reporters in HEK293.
SPLiT-seq
Split-seq is our approach to high-throughput single-cell RNA sequencing. Check out this video to see how it works. You can download a table of the oligos and detailed protocol here:
HAL
HAL is a tool for predicting the impact of human genetic variants on alternative splicing. Put in a sequence and variant and HAL will tell you whether and how isoform ratios are changed compared to the wild type.
UNCURL
UNCURL is s an unsupervised/semi-supervised pre-processing framework for scRNA-seq data. Given highly sampled/sparse transcriptomic data, UNCURL estimates the true state using a matrix factorization approach. This cleaned-up data can then be used in downstream applications such as visualizations, clustering and lineage estimation. UNCURL also allows users to provide qualitative prior information to semi-supervise the state estimation process. UNCURL is highly scalable and is shown to work on datasets with over 1 million cells.
UNCURL-App
UNCURL-App is a unified framework for interactively analyzing single-cell RNA-seq data. It is based on UNCURL for data preprocessing and clustering. It can be used to perform a variety of tasks such a unsupervised or semi-supervised preprocessing, clustering, dimensionality reduction, differential expression or interactive data analysis and visualization.
HAL is a tool for predicting the impact of human genetic variants on alternative splicing. Put in a sequence and variant and HAL will tell you whether and how isoform ratios are changed compared to the wild type.
UNCURL
UNCURL is s an unsupervised/semi-supervised pre-processing framework for scRNA-seq data. Given highly sampled/sparse transcriptomic data, UNCURL estimates the true state using a matrix factorization approach. This cleaned-up data can then be used in downstream applications such as visualizations, clustering and lineage estimation. UNCURL also allows users to provide qualitative prior information to semi-supervise the state estimation process. UNCURL is highly scalable and is shown to work on datasets with over 1 million cells.
UNCURL-App
UNCURL-App is a unified framework for interactively analyzing single-cell RNA-seq data. It is based on UNCURL for data preprocessing and clustering. It can be used to perform a variety of tasks such a unsupervised or semi-supervised preprocessing, clustering, dimensionality reduction, differential expression or interactive data analysis and visualization.