• Stars
    star
    7
  • Rank 2,294,772 (Top 46 %)
  • Language
  • Created about 8 years ago
  • Updated over 7 years ago

Reviews

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

Repository Details

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

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

Gviz_multiAlignments

R script for multiple BAM alignments viewing using Gviz (bioconductor package)
R
6
star
18

SBG-CGC_course2018

IARC course on analyzing TCGA data in the SevenBridges Genomics CancerGenomicsCloud (SBG-CGC)
R
6
star
19

table_annovar-nf

annotation of variants with annovar and nextflow
Nextflow
6
star
20

template-nf

Empty template for nextflow pipelines
HTML
5
star
21

strelka2-nf

Nextflow
4
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