bernatgel

Bernat Gel's starred repositories

data-science-at-the-command-line

Data Science at the Command Line

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oneliners

Useful bash one-liners for bioinformatics.

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

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actions

GitHub Actions for the R community

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applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

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rtweet

🐦 R client for interacting with Twitter's [stream and REST] APIs

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mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Language:NimMIT667 23 208

green-recorder

A simple screen recorder for Linux desktop. Supports Wayland & Xorg

Language:PythonGPL-3.0616 19 103

rig

The R Installation Manager

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bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

MIT450 190

dorado

Oxford Nanopore's Basecaller

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colorblindr

An R package to simulate colorblindness on R figures.

Language:RMIT302 13 17

karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

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somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Language:NimMIT254 10 124

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

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smoove

structural variant calling and genotyping with existing tools, but, smoothly.

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bioc-refcard

Bioconductor cheat sheet

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hgvs

HGVS variant name parsing and generation

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fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

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varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data

150 17 67

MutScan

Detect and visualize target mutations by scanning FastQ files directly

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IGV-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

Language:PythonGPL-3.0135 7 28

poreplex

A versatile sequenced read processor for nanopore direct RNA sequencing

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bcb731

Defense Against the Dark Arts

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beyondcell

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.

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disambiguate

Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem

Language:C++MIT27 30 15

regioneR

An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests

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SCOPE

Single-cell COPy number Estimation

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karyoploter_tutorial

Examples on how to use the karyoploteR R/Bioconductor package

10 20

HalPal

Create automatic color palettes using Halton sequences in CIE L*a*b* color space.

Language:PythonGPL-3.01 1 1