cyrilzakka/arc-institute-virtual-cell-dataset
ARC Institute Virtual Cell Challenge Please check out the official website for the challenge rules and deadlines. About For this challenge, single-cell functional genomics was used to generate approximately 300,000 single-cell RNA-seq profiles by silencing 300 carefully selected genes using CRISPR interference (CRISPRi). 10x Genomics GEM-X Flex and Illumina sequencing were used to obtain single-cell gene expression profiles. The data are split into three groups… See the full description on the dataset page: https://huggingface.co/datasets/cyrilzakka/arc-institute-virtual-cell-dataset.
ARC Institute Virtual Cell Challenge
Please check out the official website for the challenge rules and deadlines.
About
For this challenge, single-cell functional genomics was used to generate approximately 300,000 single-cell RNA-seq profiles by silencing 300 carefully selected genes using CRISPR interference (CRISPRi). 10x Genomics GEM-X Flex and Illumina sequencing were used to obtain single-cell gene expression profiles. The data are split into three groups for the Virtual Cell Challenge, to allow for training, validation of initial results, and developing a final entry for the competition.
- Training set consisting of single-cell profiles for 150 gene perturbations (~150,000 cells)
- Validation set of 50 gene perturbations, for which entrants’ predicted transcriptomic results will be used to create a live ranking leaderboard during the challenge
Training data [15GB]
Gene Expression File in AnnData H5AD format.
Obs | cell barcode-batch index | targetgene | guideid | batch | |--------------------------|-------------|----------|-------| | AAACAAGCAACCTTGTACTTTAGG-Flex101 | CHMP3 | CHMP3P1P2A\|CHMP3P1P2B | Flex101 | | TTTGGACGTGGTGCAGATTCGGTT-Flex316 | non-targeting | non-targeting00035\|non-targeting03439 | Flex316 |
Var — index of gene names to predict adfile.var.index
Index(['SAMD11', 'NOC2L', 'KLHL17', 'PLEKHN1', 'PERM1', 'HES4', 'ISG15', 'AGRN', 'RNF223', 'C1orf159', ... 'MT-ND5', 'MT-ND6', 'MT-CYB'], dtype='object', length=18080)Control Cells There are 38,176 unperturbed control cells in the training data denoted with a target_gene value of ‘non-targeting’. Competitors can optionally predict expression values for the control set during submission or copy expression values over from the training set.