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Nesli Avgan's starred repositories

scanpy

Single-cell analysis in Python. Scales to >1M cells.

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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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salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

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bowtie2

A fast and sensitive gapped read aligner

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kallisto

Near-optimal RNA-Seq quantification

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infercnv

Inferring CNV from Single-Cell RNA-Seq

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In-depth-NGS-Data-Analysis-Course

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NGS-pipeline

By study this, it won't be costly or time-consuming to customize a NGS data analysis pipeline

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ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

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ExpansionHunter

A tool for estimating repeat sizes

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single-cell-bioinformatics

Course material in notebook format for learning about single cell bioinformatics methods

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ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

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bcbioRNASeq

R package for bcbio RNA-seq analysis.

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datasets

Benchmark datasets for WGS analysis

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LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts

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