TA_sequence_similarity

Comparing BLAST and sc-RNAseq results to explore the role of sequence similarity TA

BLAST alignment comparison

Download and extract sequences
- Download_sequence_py.ipynb
- Extract_mapped_sequence.ipynb
Run BLAST
Check genes in hits
- Check_Genes_in_hits_BLAST.ipynb
- Check_Genes_in_hits_Carsten.ipynb

PCA and volcanoplot of RNAseq results
- RNAseq_PCA.ipynb
- RNAseq_volcanoplot.ipynb
Filtering Significantly Upreguated Genes that has Sequence Similarity
- RNAseq_siggenes-Lihan.ipynb
- RNAseq_siggenes-Mohamed.ipynb
GSEA / GO of upregulated genes
- GO_of_upregulated_genes.ipynb
- GSEA_of_upregulated_genes.ipynb

Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
Check_Genes_in_hits_BLAST.ipynb		Check_Genes_in_hits_BLAST.ipynb
Check_Genes_in_hits_Carsten.ipynb		Check_Genes_in_hits_Carsten.ipynb
Download_sequence_py.ipynb		Download_sequence_py.ipynb
Extract_mapped_sequence.ipynb		Extract_mapped_sequence.ipynb
GO_of_upregulated_genes.ipynb		GO_of_upregulated_genes.ipynb
GSEA_of_upregulated_genes.ipynb		GSEA_of_upregulated_genes.ipynb
README.md		README.md
RNAseq_PCA.ipynb		RNAseq_PCA.ipynb
RNAseq_siggenes-Lihan.ipynb		RNAseq_siggenes-Lihan.ipynb
RNAseq_siggenes-Mohamed.ipynb		RNAseq_siggenes-Mohamed.ipynb
RNAseq_volcanoplot.ipynb		RNAseq_volcanoplot.ipynb