gene_and_mirna

Convert.py:

bam_to_gtf: from bam to gtf
gtf_to_db: from gtf to database
gtf_to_db_all: all gtf to database by tissues
avg_rna_seq_by_tissues: average RNA-seq by tissues <average(adrenal_a, adrenal_c, adrenal_d)>

download_RNA_seq.py:

get_file_pair: get pairs by SRA (file id)
comp_fa_to_sam: fastq pair to sam file
sam_to_bam: from sam to bam
bam_to_gtf: from bam to gtf
to_bed: from fastq to gtf

Correlation_gpu.py:

get_tpm: TPM comparing to GENCODE's (v30) transcripts.

Name		Name	Last commit message	Last commit date
Latest commit History 199 Commits
.idea		.idea
exon		exon
CAP6517.py		CAP6517.py
Comparison.py		Comparison.py
Comparison_gpu.py		Comparison_gpu.py
Convert.py		Convert.py
Correlation.py		Correlation.py
Correlation2.py		Correlation2.py
Correlation_gpu.py		Correlation_gpu.py
Database.py		Database.py
DeepLearning.py		DeepLearning.py
Extract.py		Extract.py
Fantom_RNA.py		Fantom_RNA.py
Fantom_RNA_gpu.py		Fantom_RNA_gpu.py
GSEA.py		GSEA.py
Graph.py		Graph.py
Intergenic.py		Intergenic.py
Lasso.py		Lasso.py
README.md		README.md
RNA-seq_data_structure.xlsx		RNA-seq_data_structure.xlsx
Regression.py		Regression.py
Search_TSSs.py		Search_TSSs.py
Server.py		Server.py
Statistic.py		Statistic.py
Tss_map.py		Tss_map.py
Tss_map_table.py		Tss_map_table.py
Util.py		Util.py
answers.py		answers.py
cell_line.xlsx		cell_line.xlsx
cell_lines.csv		cell_lines.csv
cell_lines.txt		cell_lines.txt
columns.txt		columns.txt
compare_conv_files.py		compare_conv_files.py
corr_cl.py		corr_cl.py
corr_gpu.py		corr_gpu.py
data_eval.py		data_eval.py
data_preparation.py		data_preparation.py
deep_learning.py		deep_learning.py
dl-submit.slurm		dl-submit.slurm
download_CAGE_peaks.py		download_CAGE_peaks.py
download_RNA_seq.py		download_RNA_seq.py
expression.py		expression.py
extract_ensembl.py		extract_ensembl.py
fa_to_bed.py		fa_to_bed.py
fantom_hcage.py		fantom_hcage.py
for_test.py		for_test.py
formula6-1.gif		formula6-1.gif
formula7-1.gif		formula7-1.gif
formula7.gif		formula7.gif
gencode.py		gencode.py
gene.xlsx		gene.xlsx
high_consistent_genes.py		high_consistent_genes.py
inter_intro.py		inter_intro.py
investigate.py		investigate.py
miRNA.py		miRNA.py
mir_gene.py		mir_gene.py
phyper.py		phyper.py
position_plot.py		position_plot.py
pro-submit.slurm		pro-submit.slurm
report.py		report.py
requirements.txt		requirements.txt
set_go.py		set_go.py
set_reference_gene.py		set_reference_gene.py
split_table.py		split_table.py
sqlgpu.py		sqlgpu.py
target_genes.py		target_genes.py
tissues_fantom_rna.xlsx		tissues_fantom_rna.xlsx
to_database.py		to_database.py
validation.py		validation.py

mgcha85/gene_and_mirna

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gene_and_mirna

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