GitHub - jknightlab/mirna_pipeline: bioinformatics pipeline to analyze micro RNA sequencing data

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Name		Name	Last commit message	Last commit date
Latest commit History 165 Commits
mRNA		mRNA
ANOVA.md		ANOVA.md
Alignment_process.md		Alignment_process.md
Alignment_results.md		Alignment_results.md
Diff_expression.md		Diff_expression.md
Filtering_steps_code.md		Filtering_steps_code.md
HC_Th17_vs_AS_Th17_log2FC_scatter.png		HC_Th17_vs_AS_Th17_log2FC_scatter.png
SV_vs_nonSV.mapped_reads.png		SV_vs_nonSV.mapped_reads.png
WTCHG_189135_292_1.cutadapt_log.txt		WTCHG_189135_292_1.cutadapt_log.txt
WTCHG_189136_285_1_fastqc.trimmed.txt		WTCHG_189136_285_1_fastqc.trimmed.txt
WTCHG_189136_285_1_fastqc.txt		WTCHG_189136_285_1_fastqc.txt
Workflow_simplified.md		Workflow_simplified.md
all_samples.mapped_reads.png		all_samples.mapped_reads.png
candidates_AS_Th17_VS_AS_nonTh17.txt		candidates_AS_Th17_VS_AS_nonTh17.txt
candidates_HC_Th17_VS_AS_Th17.txt		candidates_HC_Th17_VS_AS_Th17.txt
candidates_HC_Th17_VS_AS_nonTh17.txt		candidates_HC_Th17_VS_AS_nonTh17.txt
candidates_HC_Th17_VS_HC_nonTh17.txt		candidates_HC_Th17_VS_HC_nonTh17.txt
candidates_HC_nonTh17_VS_AS_Th17.txt		candidates_HC_nonTh17_VS_AS_Th17.txt
candidates_HC_nonTh17_VS_AS_nonTh17.txt		candidates_HC_nonTh17_VS_AS_nonTh17.txt
diff_expression_AS_Th17_VS_AS_nonTh17.txt		diff_expression_AS_Th17_VS_AS_nonTh17.txt
diff_expression_HC_Th17_VS_AS_Th17.txt		diff_expression_HC_Th17_VS_AS_Th17.txt
diff_expression_HC_Th17_VS_AS_nonTh17.txt		diff_expression_HC_Th17_VS_AS_nonTh17.txt
diff_expression_HC_Th17_VS_HC_nonTh17.txt		diff_expression_HC_Th17_VS_HC_nonTh17.txt
diff_expression_HC_VS_AS.pooled.txt		diff_expression_HC_VS_AS.pooled.txt
diff_expression_HC_nonTh17_VS_AS_Th17.txt		diff_expression_HC_nonTh17_VS_AS_Th17.txt
diff_expression_HC_nonTh17_VS_AS_nonTh17.txt		diff_expression_HC_nonTh17_VS_AS_nonTh17.txt
diff_expression_public_example.png		diff_expression_public_example.png
dispersion_estimate_public_example.png		dispersion_estimate_public_example.png
dispersion_estimation.png		dispersion_estimation.png
example_dcaf6.png		example_dcaf6.png
example_lmna.png		example_lmna.png
full_candidates_AS_Th17_VS_AS_nonTh17.txt		full_candidates_AS_Th17_VS_AS_nonTh17.txt
full_candidates_HC_Th17_VS_AS_Th17.txt		full_candidates_HC_Th17_VS_AS_Th17.txt
full_candidates_HC_Th17_VS_AS_nonTh17.txt		full_candidates_HC_Th17_VS_AS_nonTh17.txt
full_candidates_HC_Th17_VS_HC_nonTh17.txt		full_candidates_HC_Th17_VS_HC_nonTh17.txt
full_candidates_HC_nonTh17_VS_AS_Th17.txt		full_candidates_HC_nonTh17_VS_AS_Th17.txt
full_candidates_HC_nonTh17_VS_AS_nonTh17.txt		full_candidates_HC_nonTh17_VS_AS_nonTh17.txt
hairpin_miRNA_all_samples_distr.png		hairpin_miRNA_all_samples_distr.png
hairpin_miRNA_all_samples_legend.png		hairpin_miRNA_all_samples_legend.png
hairpin_miRNA_all_samples_matrix_all.txt		hairpin_miRNA_all_samples_matrix_all.txt
hairpin_miRNA_all_samples_matrix_most_representes.txt		hairpin_miRNA_all_samples_matrix_most_representes.txt
hairpin_miRNA_all_samples_numbers.png		hairpin_miRNA_all_samples_numbers.png
kruskal_wallis_results		kruskal_wallis_results
kw_r.R		kw_r.R
limma_output		limma_output
limma_output_full		limma_output_full
log_fold_change_HC_Th17_VS_HC_nonTh17.png		log_fold_change_HC_Th17_VS_HC_nonTh17.png
mature_miRNA_all_samples_distr.png		mature_miRNA_all_samples_distr.png
mature_miRNA_all_samples_legend.png		mature_miRNA_all_samples_legend.png
mature_miRNA_all_samples_matrix_all.txt		mature_miRNA_all_samples_matrix_all.txt
mature_miRNA_all_samples_matrix_most_representes.txt		mature_miRNA_all_samples_matrix_most_representes.txt
mature_miRNA_all_samples_numbers.png		mature_miRNA_all_samples_numbers.png
miR-155-5p_miR-146a-5p.png		miR-155-5p_miR-146a-5p.png
miR-155-5p_miR-146a-5p_miR-210-3p.png		miR-155-5p_miR-146a-5p_miR-210-3p.png
miR-21-5p_miR-10b-5p.png		miR-21-5p_miR-10b-5p.png
miR-210-3p_miR-21-5p.png		miR-210-3p_miR-21-5p.png
miRExpress_tutorial.md		miRExpress_tutorial.md
mirna_expression_and_targets.txt		mirna_expression_and_targets.txt
mirna_matrix.txt		mirna_matrix.txt
mirna_matrix.xls		mirna_matrix.xls
mirna_matrix_no_285.xls		mirna_matrix_no_285.xls
mirna_matrix_no_285_DESeq_intput.txt		mirna_matrix_no_285_DESeq_intput.txt
mirna_selection.png		mirna_selection.png
mirna_titration_correlations.txt		mirna_titration_correlations.txt
mirna_titration_matrix.txt		mirna_titration_matrix.txt
mirna_titration_speedvac.md		mirna_titration_speedvac.md
reads_mapped_to_miRNAs.png		reads_mapped_to_miRNAs.png