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CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

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ConanVarvar

ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole genome sequencing data

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Sniffles

Structural variation caller using third generation sequencing

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cnvkit

Copy number variant detection from targeted DNA sequencing

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CHM13

The complete sequence of a human genome

NOASSERTION87100

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Language:C++BSD-3-Clause40500

CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads

Language:PythonMIT16300

ERDS

A tool for detecting CNVs from WGS data

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Jasmine

Jasmine: SV Merging Across Samples

Language:JavaMIT16300

CNVscore

Machine-learning model for the prioritization of CNVs with uncertainty estimates in rare disease patients

Language:RGPL-3.0500

SURVIVOR

Toolset for SV simulation, comparison and filtering

Language:C++MIT33300

FastQt

FastQC port to Qt5: A quality control tool for high throughput sequence data.

Language:C++GPL-3.010900

SEAL

SEAL db - Simple, Efficient And Lite database for NGS

Language:HTMLGPL-3.0800

TenXTools

Functions have access to molecule_info.h5 file from Cellranger

Language:PythonMIT400

dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

Language:C++GPL-3.08400

DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

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cellrangerRkit

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

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cellranger

10x Genomics Single Cell Analysis

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rnaseq_tutorial

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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RCA

R package for robust clustering of single cell RNA sequencing data

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umis

Tools for processing UMI RNA-tag data

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bin

My bioinfo toolbox

Language:PythonGPL-3.04800

seurat

R toolkit for single cell genomics

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AML-multistage

Code accompanying Precision oncology for acute myeloid leukemia using a knowledge bank approach

Language:HTMLGPL-3.02500

convector

CONVector tool for exon-scale CNV detection in target massively parallel sequencing (MPS) data.

Language:JavaGPL-2.0700

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

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cgpAnalyseHub

Tools to automate CGHub repository download and process with CGP analysis pipelines.

Language:PerlAGPL-3.0100

VAGrENT

A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences

Language:PerlAGPL-3.0800

cgpNgsQc

Collection of code for checking NSG sequencing results

Language:PerlAGPL-3.0300

ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing

Language:PerlAGPL-3.06500