• cisTopic

  • Referenced in 1 article [sw35766]
  • Regulatory topic modelling on single-cell ATAC-seq data. We present cisTopic, a probabilistic framework ... compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain, and transcription-factor...
  • plot2DO

  • Referenced in 1 article [sw37588]
  • types of experiments, such as ChIP-seq, ATAC-seq, and chemical cleavage mapping. In principle...
  • VplotR

  • Referenced in 1 article [sw37587]
  • package relies on cross-correlation of ATAC-seq fragment density plots to accurately map nucleosome...
  • Cistrome Data Browser

  • Referenced in 0 articles [sw41949]
  • from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays, which map the genome ... scale ChIP-seq, DNase-seq, and ATAC-seq data. First, users can query the factors ... similar ChIP-seq, DNase-seq, and ATAC-seq samples in terms of genomic interval overlaps...
  • msCentipede

  • Referenced in 0 articles [sw26450]
  • sites using chromatin accessibility data (Dnase-seq, ATAC-seq) and is written in Python2.x...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...
  • Graphviz

  • Referenced in 90 articles [sw01283]
  • Graphviz is open source graph visualization software. Graph...
  • Bioconductor

  • Referenced in 319 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • gplots

  • Referenced in 7 articles [sw04555]
  • gplots: Various R Programming Tools for Plotting Data...
  • PLINK

  • Referenced in 66 articles [sw04581]
  • PLINK is a free, open-source whole genome...
  • gcrma

  • Referenced in 97 articles [sw06104]
  • Bioconductor/R package gcrma: Background Adjustment Using Sequence Information...
  • edgeR

  • Referenced in 53 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis...
  • igraph

  • Referenced in 209 articles [sw07066]
  • igraph is a software package for complex network...
  • WGCNA

  • Referenced in 26 articles [sw07123]
  • R package WGCNA: Weighted Correlation Network Analysis. Functions...
  • BoolNet

  • Referenced in 18 articles [sw07365]
  • BoolNet: Generation, reconstruction, simulation and analysis of synchronous...
  • Cytoscape

  • Referenced in 80 articles [sw09080]
  • Cytoscape: A Software Environment for Integrated Models of...
  • COPASI

  • Referenced in 70 articles [sw12253]
  • COPASI: biochemical network simulator. COPASI is a software...
  • Dynagraph

  • Referenced in 15 articles [sw13656]
  • The Dynagraph libraries are written in platform-neutral...
  • BioNet

  • Referenced in 5 articles [sw13828]
  • The BioNet package provides an extensive framework for...
  • KEGG

  • Referenced in 280 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG...