• Stars
    star
    4
  • Rank 3,304,323 (Top 66 %)
  • Language Nextflow
  • License
    GNU General Publi...
  • Created about 7 years ago
  • Updated 9 months ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

More Repositories

1

BAM-tricks

Tip and tricks for BAM files
78
star
2

R-tricks

Tip and tricks for R
55
star
3

awesome-TCGA

Curated list of TCGA resources
51
star
4

needlestack

Multi-sample somatic variant caller
R
49
star
5

IARC-nf

List of IARC bioinformatics nextflow pipelines
44
star
6

alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline
Nextflow
25
star
7

RNAseq-nf

RNAseq analysis pipeline
HTML
22
star
8

VCF-tricks

Tip and tricks for VCF files
R
20
star
9

polysolver-singularity

Building a Singularity image of Polysolver
10
star
10

mutspec

Mutation Spectra Analysis
Perl
10
star
11

gatk4-GenotypeGVCFs-nf

Joint calling of gVCF, following GATK4 Best Practices
Nextflow
9
star
12

mutect-nf

Mutect pipeline with Nextflow
Nextflow
9
star
13

RNAseq_analysis_scripts

Scripts for RNA seq analysis
R
8
star
14

nextflow-course-2018

IARC nextflow course for pipeline users
7
star
15

medical_genomics_course

Material for medical genomics course
Dockerfile
7
star
16

gatk4-HaplotypeCaller-nf

GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping.
Nextflow
7
star
17

GDC-tricks

tricks to use the Genomics Data Commons portal from the National Cancer Institute
7
star
18

Gviz_multiAlignments

R script for multiple BAM alignments viewing using Gviz (bioconductor package)
R
6
star
19

SBG-CGC_course2018

IARC course on analyzing TCGA data in the SevenBridges Genomics CancerGenomicsCloud (SBG-CGC)
R
6
star
20

table_annovar-nf

annotation of variants with annovar and nextflow
Nextflow
6
star
21

template-nf

Empty template for nextflow pipelines
HTML
5
star
22

GVCF_pipeline-nf

Nextflow pipeline for generate GVCF from BAM with GenomeAnalysisTK with step of realignment
4
star
23

abra-nf

Nextflow pipeline for ABRA (Assembly Based ReAligner)
Nextflow
4
star
24

integration_analysis_scripts

Scripts for multi-omics integration
R
4
star
25

GATK-Alignment-nf

Perform bwa alignment and pre-processing following GATK best practices
3
star
26

purple-nf

Nextflow pipeline for CNV calling with PURPLE
Nextflow
3
star
27

Imputation-nf

Imputation pipeline
Nextflow
3
star
28

gatk4-DataPreProcessing-nf

Nextflow pipeline for pre-process BAM(s) with hg38 and GATK4
Nextflow
3
star
29

conpair-nf

Nextflow pipeline for Conpair (concordance and contamination estimator)
Nextflow
3
star
30

MESOMICS_data

Data and scripts associated with MESOMICS paper and data note
R
3
star
31

addreplacerg-nf

Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file
3
star
32

methylkey

R
2
star
33

facets-nf

Pipeline using facets for fraction and copy number estimate from tumor/normal sequencing
Nextflow
2
star
34

nextflow-hackathon-2017

2
star
35

ampliconarchitect-nf

Nextflow pipeline to discover ecDNA on cancer genomes
Nextflow
2
star
36

ITH_pipeline

Pipeline to study intra tumor heterogeneity using HATCHet, DeCiFer and ClonEvol
R
2
star
37

strelka-nf

Shell
2
star
38

EGA-tricks

tricks to use the European Genome-Phenome Archive from the European Bioinformatics Institute
2
star
39

CODEX-nf

Pipeline for copy number variant calling from Whole Exome sequencing data using CODEX
R
2
star
40

NGSCheckMate-nf

Nextflow pipeline to detect matched BAMs with NGSCheckMate
Nextflow
2
star
41

fastqc-nf

Nextflow
2
star
42

RF-mut-f

A random forest implementation to filter germline mutations of tumor-only samples
R
1
star
43

LiftOver-nf

Convert BED/VCF files between two genomes with nextflow
Groovy
1
star
44

EPIDRIVER2020

Scripts writen for EPIDERIVER project
R
1
star
45

bamsurgeon-nf

bamsurgeon with step of variant simulation encapsulated with nextflow
R
1
star
46

qualimap-nf

Nextflow
1
star
47

intro-cancer-genomics

Introduction to cancer genomics
TeX
1
star
48

LSF-tricks

Tip and tricks for IBM platform LSF HPC job scheduler
1
star
49

Methylation_analysis_scripts

R scripts for Illumina array analyses
R
1
star
50

scanMyWorkDir

Non-destructive & Informative scan of a NextFlow work folder
Shell
1
star
51

gene-fusions-nf

A nextflow pipeline to call somatic gene fusions
Nextflow
1
star
52

wsearch-nf

Microbiome analysis with usearch, vsearch and phyloseq
R
1
star
53

bam_realignment-nf

bam realignment with samtools, bwa and sambamba
1
star
54

bametrics-nf

Nextflow pipeline to compute average metrics from reads that overlap a given set of positions
Shell
1
star
55

ssvht

A set of scripts to call somatic structural variants
Perl
1
star
56

mpileup-nf

Nextflow pipeline for coverage computation with samtools mpileup (bed parallelization)
Perl
1
star
57

snpeff_annotation-nf

Annotate VCF files with SnpEff and dbSnp
Nextflow
1
star
58

PVAmpliconFinder

Perl
1
star
59

IARC-SLC-meetings

IARC Synergie Lyon Cancer bioinformatics meetings reports
1
star
60

marathon-wgs

A pipeline to study intratumor heterogeneity (ITH) with Canopy
R
1
star
61

SpatialPCAForWSIs

R
1
star
62

HaloAE

Unsupervised anomaly detection model using a Halonet auto-encoder.
Python
1
star
63

PRSice-nf

Pipeline to compute polygenic risk scores
Nextflow
1
star
64

data_test

Small data files to test IARC nextflow pipelines
Perl
1
star