Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
awesome-deep-learning-single-cell-papers
https://github.com/OmicsML/awesome-deep-learning-single-cell-papers
- [Single Cell Best Practices
- [Basics of Single-Cell Analysis with Bioconductor
- 2022 Nature Methods
- [CSCI 1850 Deep Learning in Genomics
- [Machine Learning in Genomics: Dissecting Human Disease Circuitry
- [ANALYSIS OF SINGLE CELL RNA-SEQ DATA
- [Analysis of single cell RNA-seq data, www.singlecellcourse.org - step-by-step scRNA-seq analysis course. R-based, with code examples, explanations, exercises. From alignment (STAR) and QC (FASTQC) to introduction to R, SingleCellExperiment class, `scater` object, data exploration (reads, UMI), filtering, normalization (`scran`), batch effect removal (`RUV`, `ComBat`, `mnnCorrect`, GLM, `Harmony`), clustering and marker gene identification (`SINCERA`, `SC3`, tSNE, `Seurat`), feature selection (`M3Drop::M3DropConvertData`, `BrenneckeGetVariableGenes`), pseudotime analysis (`TSCAN`, `Monocle`, diffusion maps, `SLICER`, `Ouija`, `destiny`), imputation (`scImpute`, `DrImpute`, `MAGIC`), differential expression (Kolmogorov-Smirnov, Wilcoxon, `edgeR`, `Monocle`, `MAST`), data integration (`scmap`, cell-to-cell mapping, `Metaneighbour`, `mnnCorrect`, `Seurat`'s canonical correllation analysis). Search for scRNA-seq data ([scfind](https://github.com/hemberg-lab/scfind) R package), as well as [Hemberg group’s public datasets](https://hemberg-lab.github.io/scRNA.seq.datasets/). [Seurat chapter](https://scrnaseq-course.cog.sanger.ac.uk/website/seurat-chapter.html). ["Ideal" scRNA-seq pipeline](https://scrnaseq-course.cog.sanger.ac.uk/website/ideal-scrnaseq-pipeline-as-of-oct-2017.html). [Video lectures](https://www.youtube.com/watch?list=PLEyKDyF1qdOYAhwU71qlrOXYsYHtyIu8n&v=56n77bpjiKo). <details>
- 2023 Biophysics Reviews
- [foundation-model-single-cell-papers
- 2024 ICLR
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 arxiv
- 2023 bioRxiv
- 2023 Nature
- 2023 Nature Methods
- 2023 bioRxiv
- 2023 arxiv
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 Bioinformatics
- 2023 Nature
- 2023 arxiv
- 2023 arxiv
- 2023 arxiv
- 2023 iSchience tGPT
- 2023 bioRxiv
- 2023 Github
- 2023 blog
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 Nature Biotechnology
- 2022 arxiv
- 2022 Briefings in Bioinformatics
- 2022 Nature Machine Intelligence
- 2022 bioRxiv
- 2022 Bioinformatics
- 2021 PNAS
- 2021 Bioinformatics
- 2021 Arxiv, 576 citations
- 2021 Arxiv, 1111 citations
- 2024 Brief Bioinform
- 2024 biorxiv
- 2024 biorxiv
- 2024 biorxiv
- 2024 Cell - 9.pdf)
- 2023 ICCV
- 2023 biorxiv
- 2023 biorxiv Diffusion
- 2023 biorxiv GAN
- 2023 Nature Diffusion Model
- 2023 biorxiv Diffusion Model
- 2023 biorxiv GAN
- 2023 biorxiv Diffusion Model
- 2024 ICLR workshop NLP+Gene Expression
- 2024 Nature Biotechnology Image+Gene Expression
- 2023 arxiv Image+Gene Expression
- 2023 arxiv multimodal
- 2023 biorxiv multimodal
- 2023 biorxiv Image+Gene Expression
- 2023 biorxiv Image+Gene Expression
- 2023 biorxiv
- 2021 CVPR - chefer/Transformer-Explainability)
- 2021 ICML
- 2019 ACL
- 2024 biorxiv
- 2023 biorxiv
- 2023 biorxiv
- 2023 biorxiv
- 2023 arxiv survey from CS field
- 2023 ICML Reference from CS field
- 2023 arxiv multimodalities Reference from CS field
- 2023 arxiv multimodalities Reference from CS field
- 2023 arxiv multimodalities Reference from CS field
- 2023 KDD Reference from CS field
- 2023 arxiv Reference from CS field
- 2023 Nature Communications
- 2023 bioRxiv
- 2023 Nature Methods
- 2022 bioRxiv
- 2022 ICLR Reference from CS field
- 2022 NeurIPS spatial-temporal single-cell -> spatial-temporal video
- 2022 arxiv, image-gene expression contrastive learning
- 2020 ICLR, image-gene expression pretraining
- 2019 AAAI, image-gene expression pretraining
- 2023 Nature Methods
- 2023 ICLR
- 2024 ICLR
- 2024 Nature Methods
- 2023 biorxiv
- 2023 NeurIPS
- 2023 Nature Methods
- 2023 Nature Methods
- 2023 Mol Syst Biol
- 2023 biorxiv
- 2023 Nature
- 2023 biorxiv Diffusion Model
- 2023 ICLR
- 2022 arxiv
- 2022 arxiv
- 2022 NeurIPS
- 2022 biorxiv
- 2021 biorxiv
- 2019 Nature Methods
- 2023 Genome Biology
- 2023 medrxiv
- 2023 Nature Methods
- 2023 Molecular System Biology
- 2023 Genes
- 2023 Nature Communications
- 2023 Nature Reviews Clinical Oncology
- [Tool Summary
- 2024 biorxiv
- 2024 Nature Methods
- 2023 Nucleic Acids Research
- 2023 Github
- 2023 biorxiv
- 2023 Nature
- 2023 Nature
- 2023 Nature Medicine
- 2022 Nucleic Acids Research
- [Cellxgene Datasets: 546 datasets by 2022
- 2022 Nature Methods
- 2022 bioRxiv
- 2022 Nature Biotechnology
- 2022 bioRxiv
- 2022 Nature Communications
- [Chanzuckerberg: An interactive explorer for single-cell transcriptomics data
- [UCSC Cell Browser
- [Cytoscape
- [UCSC Xena
- [ASAP: Automated Single-cell Analysis Pipeline
- [GenePattern
- [Loopy Browser
- 2023 biorxiv
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 bioRxiv
- 2023 Genome Biology
- 2023 Nature Communications
- 2023 bioRxiv
- 2023 Genome Biology
- 2023 Nature Communications
- 2023 bioRxiv
- 2023 bioRxiv
- 2022 Nature Communications
- 2022 Nature Methods
- 2022 Nature Methods
- 2022 BioRxiv
- 2022 Briefings in Bioinformatics
- 2022 Nucleic Acids Research
- 2021 Frontiers in Genetics
- 2021 Nature Communications
- 2021 Genome Biology
- 2020 Nature Methods
- 2020 Genome Biology
- 2020 Nature Biotechnology
- 2019 Nature Methods
- 2019 Narure Methods
- 2024 Nature Communications
- 2023 Nature Methods
- 2023 biorxiv
- 2023 Bioinformatics
- 2023 Science
- 2023 Nature Methods
- 2022 BioRxiv
- 2022 BioRxiv
- 2022 bioRxiv
- 2019 Cell
- 2023 Genome Research
- 2021 Nature Communications
- 2018 Nature Communications
- 2023 Nature Machine Intelligence
- 2023 Genome Biology
- 2023 Nature Methods
- 2023 bioRxiv
- 2021 Current Opinion in Systems Biology
- 2020 Nature Communications
- 2019 Nature Methods
- 2018 Nature Methods
- 2023 Bioinformatics
- 2020 Genomy Biology
- 2020 Nature Biotechnology
- 2019 Nature Methods, **Harmony**
- 2018 Nature Biotechnology, **CCA**
- 2018 Nature Biotechnology, **Mutual Nearest Neighbors**
- 2018 Nature Methods
- 2017 Nature Biotechnology
- 2023 bioRxiv
- 2023 bioRxiv
- 2022 Nature Biomedical Engineering
- 2022 Nature Communications
- 2024 Nature Reviews Genetics
- 2024 bioRxiv
- 2024 Pac Symp Biocomput
- 2023 Cell Systems
- 2023 Nature Biotechnology
- 2022 bioRxiv
- 2022 Nature Biotechnology
- [paper
- 2021 Bioinformatics
- 2020 Nature Methods
- 2020 Nature Communications
- 2018 Nature
- 2023 arxiv
- 2023 Bioinformatics
- 2022 Nature Machine Intelligence
- 2022 Nature Biotechnology
- 2022 Biorxiv
- 2022 Bioinformatics
- 2022 Briefings in Bioinformatic
- 2020 Nature Methods
- 2019 Genome Biology
- 2017 Cell Syst
- 2018 Nature Communications
- 2019 Genome Biology
- 2018 Cell - 4)
- 2018 Genome Biology
- 2021 PLOS Computational Biology
- 2021 Nature Communications
- 2021 iScience - 8)
- 2022 PLOS ONE
- 2023 Nature Genetics
- 2023 bioRxiv
- 2022 Genome Research
- 2022 Nature Communications Biology
- 2022 Genome Biology
- 2022 Nature Communications
- 2022 Nature Computational Science
- 2022 Frontiers in Genetics
- 2021 Nature Methods
- 2021 Nature Biotechnology
- 2021 Biorxiv
- [Tool
- 2021 Biorxiv
- 2020 Biorxiv
- 2018 Nature Methods
- 2018 Nature Biotechnology
- 2008 Journal of Statistical Mechanics
- 2019 Nature Methods
- 2018 Nature Methods
- 2020 Bioinformatics
- 2021 Nature Biotechnology
- 2021 Molecular Systems Biology
- 2022 bioRxiv Preprint
- 2023 biorxiv
- 2022 Cytometry A - Lab/MIRIAM)(MIRIAM)
- 2021 Nature Biotechnology
- [paper - publish)
- 2021 Nature Biotechnology
- 2021 Nature Biotechnology - to-deepcell)(Memser)
- 2021 Nature Methods
- 2021 Molecular Systems Biology
- 2020 Nature Communications - GUI)
- 2020 Medical Image Analysis
- 2016 Computational Biology - tf) (Deepcell)
- 2023 Genome Biology
- 2023 BioRxiv
- 2023 BioRxiv
- 2023 BioRxiv
- 2022 Nature Biotechnology
- 2022 Nature Communications
- 2022 Nature Biotechnology
- 2022 Biorxiv
- 2022 Nature Biotechnology
- 2022 Nature Cancer
- 2022 Nature Communications
- 2022 Nature Biotechnology
- 2021 Briefings in Bioinformatics
- 2021 Genome Research
- 2021 Genome Biology
- 2021 Nucleic Acids Research
- 2021 Nature Biotechnology
- 2019 Nature Communications
- 2019 Science
- 2023 biorxiv
- 2023 Nature Methods
- 2023 Nature Methods
- 2023 Nature Communications
- 2023 Nature Biotech
- 2022 Nature Method
- 2022 Brief Bioinform
- 2022 Nature Communications
- 2022 Science
- 2022 Bioinformatics
- 2022 Cancers
- 2021 Nucleic Acids Research
- 2021 BMC Bioinformatics
- 2021 Genome Research
- 2020 BMC Bioinformatics
- 2020 Bioinformatics
- 2020 Nature Communications
- 2019 Nucleic Acids Research
- 2019 Nucleic Acids Research
- 2019 Bioinformatics
- 2019 Cell Systems
- 2019 Genome Biology
- 2023 Bioinformatics
- 2023 bioRxiv
- 2022 BMC Bioinformatics
- 2022 Bioinformatics
- 2022 AAAI
- 2022 Briefings in Bioinformatics
- 2022 Bioinformatics
- 2022 Nature Computational Science
- 2021 Nature Communications
- 2020 NAR Genomics and Bioinformatics
- 2020 Nature Communications
- 2019 Nature Machine Intelligence
- 2017 Nature Communications
- 2024 Nature Biotechnology
- 2018 IJCAI
- 2021 NPJ Digital Medicine
- 2022 Biocumputing
- 2022 CHIL '20: Proceedings of the ACM Conference on Health, Inference, and Learning
- 2023 Nature Biotechnology
- 2023 Nature Communications
- 2023 biorxiv
- 2023 Nature Biotechnology
- 2023 Nature Biotechnology
- 2023 Briefings in Bioinformatics
- 2022 PMLR
- 2022 Nature Biotechnology
- 2022 Nature Communications
- 2022 Genome Biology
- 2018 ICML
- 2019 PLoS computational biology
- 2020 Bioinformatics
- 2021 Nature communications
- 2021 PLoS Computational Biology
- 2021 Genome biology
- 2021 Cell reports methods
- 2021 Briefings in Bioinformatics
- 2021 Bioinformatics
- 2022 Nature Biotechnology
- 2022 Bioinformatics
- 2022 SIGKDD
- 2022 Genome biology
- 2019 Biorxiv
- 2021 Biorxiv
- 2022 Biorxiv
- 2022 Biorxiv
- 2019 NeurIPS multi-lingual pretraining for multi-omics
- 2024 Nature Communications
- 2023 bioRxiv scTranslator
- 2023 Advanced Science
- 2022 JCB
- 2022 RECOMB
- 2020 PNAS
Programming Languages