histone-modifications

There are 0 repository under histone-modifications topic.

• crazyhottommy / ChIP-seq-analysis

  ChIP-seq analysis notes from Ming Tang

  chip-seqhistone-modificationstranscription-factor-binding
  Language:Python 712
• chromoformer

  dohlee / chromoformer

  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

  bioinformaticsdeep-learningtransformerhistone-modificationsgene-expressionartificial-intelligencegenomicsepigenomicstranscriptomics
  Language:Python 30

• satijalab / scChromHMM

  🧬 🦀 A fast and efficient tool to perform a genome wide Single cell Chromatin State Analysis using multimodal histone modification data.

  single-cellchromatin-statehistone-modifications
  Language:Rust 24

• YosefLab / epitome

  Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility

  chromatin-accessibilitydnase-seqatac-seqepigenetic-eventstranscription-factorshistone-modifications
  Language:Python 10

• Bohdan-Khomtchouk / geneSpark

  geneSpark is a bioinformatics software program written in Python and Apache Spark for big data epigenetic histone modification ChIP-seq analysis.

  bioinformaticscomputational-biologyapache-sparkpythonchip-seqhistone-modifications
  Language:Python 5

• tagtag / TDbasedUFE

  This is a R package that intends to perform all the features possible by tensor decomposition based unsupervised feature extraction

  bioinformaticsdna-methylationgene-expression-profileshistone-modificationsmultiomicstensor-decomposition
  Language:R 5

• neurogenomics / CHAS

  Cell type-specific Histone Acetylation Score

  epigenomicsdeconvolutionhistone-modifications
  Language:R 3

• robert-yaman / DeepChrome_tensorflow

  Using CNNs to model affect of histone modification on gene expression

  gene-expressionhistone-modificationsconvolutionbioinformatics
  Language:Python 3

• Bohdan-Khomtchouk / ENCODE_histone_geneXtendeR_analysis

  geneXtendeR analysis on 198 human histone modification ChIP-seq ENCODE datasets

  bioinformaticschip-seqcomputational-biologyhistone-modifications
  Language:R 2

• sartorlab / chipenrich

  This is the fork of the Bioconductor-mirror repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/chipenrich.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=chipenrich.

  chip-seqgeneset-enrichmenttranscription-factorshistone-modifications
  Language:R 2

• atnick484 / simr2019

  The abstract and poster for my internship under the Stanford Institutes of Medical Research at the Khatri Lab in the summer of 2019. More code/scripts can be made available upon request (I used primarily R and SQL)

  histone-modificationschip-seqgenesheatmapspeaks
  1

• miamib34ch / HSE-Bioinformatics

  Practical and home works in the discipline Bioinformatics.

  bioinformaticschromhmmgene-predictiongenetic-map-visualizationgenome-analysisgenome-annotationgenome-assemblyhi-chistone-modificationsmethylation-analysisphylogenetic-treesquadruplexesrna-seq-analysissequence-alignmentsingle-cell-rna-seqsnpspython
  Language:HTML 1

• benja0x40 / Tightrope

  ChIP-seq normalization according to background reads density. (R package)

  normalizationnext-generation-sequencingbioinformaticsgenomicschip-seqchromatinhistone-modificationshistone-variantsr
  Language:R 0

• ly-zhu / CRNN-gene-expression-with-histone-modifications

  Gene expression prediction with Convolutional Recurrent Neural Networks

  crnnconvolutional-neural-networksrecurrent-neural-networksgene-expression-predictionhistone-modifications
  Language:Python 0

• shaorray / Nucount

  A nucleosomal reads counting tool

  chip-seqexpectation-maximizationhistone-modificationsnucleosome
  Language:R 0

• curlyphysicist / BIOINFO

  my master's research in bioinformatics

  bioinformaticshistone-modificationscnn-keras
  Language:Jupyter Notebook

• MahShaaban / segmenterNote

  A technical note to describe the segmenter package

  chipseqchromatine-segmentationhistone-modifications
  Language:HTML
• CUT_n_TAG

  neurogenomics / CUT_n_TAG

  Preprocessing pipeline for CUT&TAG data.

  epigenomicshistone-modificationsbenchmarkingencode
  Language:HTML

• neurogenomics / CUTnTag-benchmarking-analysis

  Processing, benchmarking and analysis of CUT&Tag against ENCODE ChIP-seq.

  cutandtag-seqepigenomicshistone-modifications
  Language:HTML

• rj60001 / HMI

  Histone Modification Interpreter

  biologybiological-sequencesbiological-structuresgeneticsgenetic-programmingepigeneticshistone-modifications
  Language:PHP

• YogiOnBioinformatics / ChIP-Seq-Analysis-Nanog-and-H3K27Ac

  Independent project I undertook to perform a full ChIP-Seq analysis of the transcription factor Nanog in Zebrafish embryos.

  bashchip-seqcomputational-genomicsdanio-reriodeeptoolsdevelopmental-biologyhigh-performance-computinghisat2histone-modificationslinuxsrazebrafish