snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
V Bhardwaj, S Heyne, K Sikora, L Rabbani… - …, 2019 - academic.oup.com
Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable
analysis workflows are of wide interest. Here we present snakePipes, a workflow package …
analysis workflows are of wide interest. Here we present snakePipes, a workflow package …
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data
Abstract ChIP-Atlas (https://chip-atlas. org) is a web service providing both GUI-and API-
based data-mining tools to reveal the architecture of the transcription regulatory landscape …
based data-mining tools to reveal the architecture of the transcription regulatory landscape …
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
F Marini, A Ludt, J Linke, K Strauch - BMC bioinformatics, 2021 - Springer
Background The interpretation of results from transcriptome profiling experiments via RNA
sequencing (RNA-seq) can be a complex task, where the essential information is distributed …
sequencing (RNA-seq) can be a complex task, where the essential information is distributed …
iGEAK: an interactive gene expression analysis kit for seamless workflow using the R/shiny platform
Background The use of microarrays and RNA-seq technologies is ubiquitous for
transcriptome analyses in modern biology. With proper analysis tools, the differential gene …
transcriptome analyses in modern biology. With proper analysis tools, the differential gene …
pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Abstract We present pipeComp (https://github. com/plger/pipeComp), a flexible R framework
for pipeline comparison handling interactions between analysis steps and relying on multi …
for pipeline comparison handling interactions between analysis steps and relying on multi …
SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision
MS Wiewiórka, A Messina, A Pacholewska… - …, 2014 - academic.oup.com
Many time-consuming analyses of next-generation sequencing data can be addressed with
modern cloud computing. The Apache Hadoop-based solutions have become popular in …
modern cloud computing. The Apache Hadoop-based solutions have become popular in …
RASflow: an RNA-Seq analysis workflow with Snakemake
X Zhang, I Jonassen - BMC bioinformatics, 2020 - Springer
Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq
data are being generated giving novel insight into gene expression and regulation. Prior to …
data are being generated giving novel insight into gene expression and regulation. Prior to …
BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
AV Kartashov, A Barski - Genome biology, 2015 - Springer
High-throughput sequencing has revolutionized biology by enhancing our ability to perform
genome-wide studies. However, due to lack of bioinformatics expertise, modern …
genome-wide studies. However, due to lack of bioinformatics expertise, modern …
Practical guidelines for the comprehensive analysis of ChIP-seq data
Mapping the chromosomal locations of transcription factors, nucleosomes, histone
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …
Benchmarking UMI-based single-cell RNA-seq preprocessing workflows
Background Single-cell RNA-sequencing (scRNA-seq) technologies and associated
analysis methods have rapidly developed in recent years. This includes preprocessing …
analysis methods have rapidly developed in recent years. This includes preprocessing …