CRISPRCloud2 – Deconvolution of your CRISPR pooled screening data

CRISPRCloud2

:: DESCRIPTION

CRISPRCloud2 is a user-friendly cloud-based analysis platform for the deconvolution of CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats) pooled screening data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Jeong HH, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z.
CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution.
Bioinformatics. 2017 Sep 15;33(18):2963-2965. doi: 10.1093/bioinformatics/btx335. PMID: 28541456; PMCID: PMC5870715.

Syzygy 1.2.7 – SNP and Indel Calling for pooled and individual Targeted Resequencing Studies

Syzygy 1.2.7

:: DESCRIPTION

Syzygy is a targeted sequencing post processing analysis tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant.

::DEVELOPER

Rivas Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Syzygy

:: MORE INFORMATION

Citation

Rivas et al. (2011),
Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease“,
Nature Genetics 43, 1066–1073 (2011)

MAGeCKFlute 1.6.0 – Analysis of pooled CRISPR Functional Genetic Screens

MAGeCKFlute 1.6.0

:: DESCRIPTION

MAGeCKFlute is designed to support downstream analysis, utilizing the gene summary data provided through MAGeCK or MAGeCK-VISPR. Quality control, normalization, and screen hit identification for CRISPR screen data are performed in pipeline. Identified hits within the pipeline are categorized based on experimental design, and are subsequently interpreted by functional enrichment analysis.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Bioconductor

:: DOWNLOAD

MAGeCKFlute

:: MORE INFORMATION

Citation

Nat Protoc. 2019 Mar;14(3):756-780. doi: 10.1038/s41596-018-0113-7.
Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute.
Wang B, et al.

PoPoolation 1.2.2 / PoPoolation2 1.201 / PoPoolation TE 1.02 – Analyse Pooled Next Generation Sequencing data

popoolation 1.2.2 / PoPoolation2 1.201 / PoPoolation TE 1.02

:: DESCRIPTION

PoPoolation is a collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals

PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences.

PoPoolation TE is a quick and simple pipeline for the analysis of transposable element insertions in (natural) populations using next generation sequencing.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 popoolation , PoPoolation2

:: MORE INFORMATION

Citation:

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.
Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C, Schlštterer C.
PLoS One. 2011 Jan 6;6(1):e15925.

Kofler,R.,Vinay Pandey, R. & Schloetterer, C
PoPoolation2: Identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq);
Bioinformatics; Vol. 27 no. 24 2011, pages 3435–3436; doi:10.1093/bioinformatics/btr589

Robert Kofler, Andrea Betancourt and Christian Schloetterer (2012):
Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster;
PLoS Genet 8(1): e1002487. doi:10.1371/journal.pgen.1002487