WebAssembly modules for genomics
javascript bioinformatics genomics webassembly awk jq sed grep bedtools samtools bowtie2 minimap2 seqtk
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Oct 24, 2025 - HTML
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bedtools
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gia: Genomic Interval Arithmetic
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Aug 21, 2024 - Rust
Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads
genome fasta fastq bedtools samtools genome-analysis bwa-mem transposons genome-assembly multiple-sequence-alignment transposable-element consensus-sequences
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Nov 25, 2024 - Shell
Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. ...
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Aug 9, 2018 - HTML
Python Library for data analysis based on GMQL
python java bioinformatics scala big-data binder genomics anaconda pypi jupyter-notebook bioinformatics-pipeline bedtools bioinformatics-analysis gmql bioinformatics-tool
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Dec 1, 2021 - Python
RNAseq pipeline for alternative splicing junctions
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Apr 23, 2025 - R
A beginner’s guide to Bioinformatics
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Sep 22, 2025
program to make bed12 files from bed 6 files based on the name col of the bed6 file.
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Apr 8, 2019 - Shell
Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools
rna-seq network assembly bloom-filter conda pandas python3 biopython bioconda kmer transcriptome transcriptomics bedtools exon abyss splice-graphs biobloomtools abyss-bloom
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Jul 28, 2020 - Python
Useful NGS utilities for everyday use in the form of stand-alone tool.
java genomics computational-biology vcf interval-tree bed bedtools vcftools dataanalysis ngs-analysis vcf-filtering snp-variants deletion-variants insertion-variants vcf-comparator
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Dec 2, 2022 - Java
RNA-seq pipeline in R/Bash enables QC, alignment, read counting, and differential expression using Bioconductor; reproducible workflow on Ubuntu with Conda. 🐙
snakemake pipeline genomics notebook panel jupyter-notebook bioinformatics-pipeline transcript rnaseq read-counts illumina bedtools salmon rna-seq-analysis rsem gff ngs-analysis snpeff
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Oct 24, 2025 - R
Plant DNA Annotation and Preparation for Neural Networks
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Mar 25, 2024 - Python
Assembly of RNA transcriptome, differential expression analysis, identification of lncRNA candidates based on genomic context and protein coding potential.
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Feb 9, 2024 - Shell
This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.
rna-seq multiqc star bedtools rna-seq-analysis samtools featurecounts bamtools htseq-count stringtie bulk-rna-seq nextflow-pipelines bulk-sequencing
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Nov 22, 2024 - Nextflow
bedtools environment containerized for singularity
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May 22, 2018 - Shell
Pipeline for automated genomic variant analysis in inherited diseases, integrating alignment, variant calling, and quality control
bioinformatics pipeline genomics ngs computational-biology vcf multiqc variant-calling genetic-analysis bedtools samtools bowtie2 fastqc freebayes qualimap
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May 22, 2024 - Shell
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