ChoudalakisM

ChoudalakisM's Stars

• erkutilaslan/biovizR

  biovizR: An R package to easily analyze and visualize biological data designed for wet-lab scientists.

  Language:R1

• MultiQC/MultiQC

  Aggregate results from bioinformatics analyses across many samples into a single report.

  Language:JavaScript1.2k598

• cxli233/FriendsDontLetFriends

  Friends don't let friends make certain types of data visualization - What are they and why are they bad.

  Language:R6.3k231

• CFIA-NCFAD/wgscovplot

  The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth information, variants and DNA Gene features

  Language:JavaScript176

• ossu/bioinformatics

  :microscope: Path to a free self-taught education in Bioinformatics!

  5.4k900

• langmead-lab/FORGe

  Code for building and testing variant ranking strategies

  Language:Python162

• ewonglab/enhancer_turnover

  Code used for the project "DNA replication timing predicts transcription factor binding and the rate of enhancer turnover"

  Language:R1

• crazyhottommy/ChIP-seq-analysis

  ChIP-seq analysis notes from Ming Tang

  Language:Python741294

• j-andrews7/awesome-bioinformatics-benchmarks

  A curated list of bioinformatics bench-marking papers and resources.

  31057

• jtleek/datasharing

  The Leek group guide to data sharing

  6.5k243k

• mhammell-laboratory/TElocal

  A package for quantifying transposable elements at a locus level for RNAseq datasets.

  Language:Python238

• inutano/pfastq-dump

  parallel-fastq-dump implementation in bash script

  Language:Shell406

• riasc/visualgraphx

  VisualGraphX, a web-based visualization tool for large-scale graphs.

  Language:JavaScript2

• Dfam-consortium/RepeatMasker

  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

  Language:Perl22850

• nf-core/rnaseq

  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

  Language:Nextflow875697

• deweylab/RSEM

  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

  Language:C++409118

• fastplotlib/fastplotlib

  Next-gen fast plotting library running on WGPU using the pygfx rendering engine

  Language:Python39533

• ZjGaothu/OpenAnnotatePy

  A python package for efficiently annotating the chromatin accessibility of genomic regions. For more information, please refer to the web: http://health.tsinghua.edu.cn/openannotate/

  Language:Jupyter Notebook2

• lh3/minipileup

  Simple pileup-based variant caller

  Language:C796

• amyfrancis97/DrivR-Base

  Language:R3

• getzlab/rnaseqc

  Fast, efficient RNA-Seq metrics for quality control and process optimization

  Language:C++14619

• scottgroup/coco

  CoCo: Count Corrector for nested genes and multi-mapped reads

  Language:Python4

• fedorrik/HumAS-HMMER_for_AnVIL

  Language:Awk51

• enigene/HumAS-HMMER

  Generates monomeric annotations of high order repeats of human alpha satellites.

  Language:Shell4

• arozanski97/CDR-Finder

  CDR-Finder

  Language:Python41

• jsun9003/PSPHunter

  A Machine Learning Model to Predict Phase Separation Driving Residues

  Language:Perl53

• cstritt/detettore

  A program to detect transposable element polymorphisms

  Language:Python81

• wyang17/SQuIRE

  Software for Quantifying Interspersed Repeat Expression

  Language:Python4828

• FenyoLab/transposcope

  Language:Python81

• FenyoLab/L1EM

  Estimate locus specific human LINE-1 expression.

  Language:Python319