Cross-Speices Brain Atlas in the light of evolution

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Bodhi

Provides online deconvolution, cell-type prediction, and other functions for RNA-seq data across 200 species, with six specialized submodules.

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: In2Cell; Deconvolution of bulk RNA-seq for 300+ species: In2Cell builds dynamic references by integrating 300+ species TimeTree and 100 species brain scRNA-seq signatures, facilitating nonnegative least squares-based prediction of bulk RNA-seq cell type compositions.

: SpaceTeller; Spatial transcriptomics deconvolution of bulk RNA-seq for different species: SpaceTeller integrates in2Cell and Bulk2Space to provide an effective solution for deconvolving bulk RNA-seq data at ST resolution.

: MissGene; Cross-species perturbation prediction: MissGene combines GRBBoost2, DEG analysis, E-test, and transfer learning to infer altered gene expressions in cross-species scRNA-seq data.

: CamPred; Cross-species automatic cell-type Prediction: guided by TimeTree that depicts distances between 300+ species, CamPred relies on transfer learning from dynamic species references to annotate cell types of query species.

: Gapbridger; Bridging development gaps at spatial transcriptomic resolution: GapBridger uses a bi-directional optimal transport algorithm to infer spatial transcriptomics patterns between two timepoints of evolution.

: Teddi; Teddi, Time Efficient Data Downsampling by Integrating distance, complexity and gini index

Part01: Deconvolution of bulk RNA-seq for 300+ species

In2Cell

Part02: Spatial transcriptomics deconvolution of bulk RNA-seq for different species

SpaceTeller

SpaceTeller Demo1

Part03: Cross-species perturbation prediction

MissGene

Cross-species perturbation prediction Demo1

Part04: Cross-species automatic cell-type Prediction

CamPred

Part05: Bridging development gaps at spatial transcriptomic resolution

Gapbridger

Part06: Teddi, Time Efficient Data Downsampling

Teddi

In2Cell

SpaceTeller

MissGene

CamPred

Gapbridger

Teddi