johandahlberg / awesome-10x-genomics
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
☆84Updated 6 years ago
Alternatives and similar repositories for awesome-10x-genomics:
Users that are interested in awesome-10x-genomics are comparing it to the libraries listed below
- Battenberg algorithm and associated implementation script☆52Updated 4 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- R package for bcbio RNA-seq analysis.☆62Updated 6 months ago
- Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).☆92Updated 7 years ago
- ☆67Updated last year
- Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.☆51Updated 6 years ago
- Very simple, pure python, BAM file reader☆79Updated 6 years ago
- nucleosome calling using ATAC-seq☆106Updated 4 years ago
- Unsorted scripts for bioinformatics☆60Updated 3 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆43Updated 2 years ago
- bradner lab computation pipeline scripts☆54Updated 3 years ago
- Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19☆74Updated 8 months ago
- Publication quality NGS track plotting☆111Updated 2 years ago
- An R package for inferring the subclonal architecture of tumors☆117Updated last year
- Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency☆147Updated 4 months ago
- ☆116Updated last year
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 3 years ago
- A tool for bigWig files.☆119Updated 6 years ago
- Tip and tricks for BAM files☆85Updated 6 years ago
- Relevant papers for CNV and SV approaches☆94Updated 4 months ago
- Transcript quantification import for modular pipelines☆137Updated last year
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆77Updated 5 years ago
- A toolkit for QC and visualization of ATAC-seq results.☆68Updated 2 months ago
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆65Updated 4 years ago
- Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…☆55Updated 5 years ago
- An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)☆111Updated last month
- identifying mutational significance in cancer genomes☆61Updated 2 years ago
- optimization of ribosome P-site positioning in ribosome profiling data☆49Updated last month
- microRNA profiling pipeline☆75Updated 3 years ago
- Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps☆124Updated 6 years ago