miARma-seq: a comprehensive tool for miRNA, mRNA and circRNA analysis
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Jun 29, 2025 - Perl
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mirna-seq
Here are 18 public repositories matching this topic...
Bioinformatics Pipeline
rna-seq snakemake pipeline metagenomics methylation data-analysis amplicon tcga-data geo-data mirna-seq
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Oct 7, 2022 - R
An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
quality-control rna-seq chip-seq whole-exome-sequencing whole-genome-sequencing single-cell-rna-seq mirna-seq
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Jul 13, 2023 - Python
An open-source R package to comprehensively explore the role of impaired miRNA regulatory networks in complex biological conditions.
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Feb 20, 2026 - R
scripts and resources for performing miRNA sequencing analysis using tools like mirPRo and miRDeep2. Explore the code to process reads, map them to the genome, quantify known miRNAs, identify novel miRNAs, and browse the results
bioinformatics next-generation-sequencing rna-seq-analysis mirna mirna-seq gene-expression-analysis mirna-sequencing small-rna-analysis
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Jun 9, 2023 - Shell
miRSim Synthetic Sequence Simulator
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May 10, 2023 - Jupyter Notebook
An awesome microRNA-sequencing pipeline
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Dec 15, 2025 - Python
Scripts of Final Master Project
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Sep 7, 2023 - R
Reproducible Bash pipeline for miRNA precursor analysis using miRBase v22 and SeqKit. Filters by organism and gene target, converts RNA→DNA, and exports GC content and length metrics as TSV and Markdown reports. Configurable via CLI args.
bash bioinformatics reproducible-research biochemistry bash-scripting c-elegans mirbase mirna-seq seqkit
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Apr 9, 2026 - Shell
multiMiR package in R, providing gene-miRNA-lncRNA interactions for ceRNA network construction
rstudio cerna mirna-mrna-interaction mirna-targets mirna-database mirna-seq lncrna-rna gene-mirna-lncrna
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Aug 22, 2024 - R
R package to predict gene feed forward loops using mediation analysis. Analyses integrate observed miRNA and mRNA expression data and database information on gene interactions.
transcription-factors gene-expression gene-regulation mediation-analysis gene-network gene-regulatory-network gene-interaction-networks mirna-seq mrna-seq
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Jun 8, 2022 - R
Involvement of Extracellular Vesicle-derived miRNA clusters in Developing Healthy and Rett Syndrome Brain Organoids
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Feb 6, 2025 - R
All the R scripts I used during my time as a grad student at Clemson University
rna-seq pearson-correlation protein-expression leafcutter mirna-seq stability-predictions western-blot
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Nov 8, 2023 - R
Interactive Shiny app for miRNA differential expression analysis, visualization, enrichment, machine learning classification, and power analysis — built for researchers and bioinformaticians
docker machine-learning bioinformatics shiny data-visualization singularity deseq2 r-language enrichment-analysis mirna power-analysis mirna-seq
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Jan 13, 2026 - R
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