arabidopsis

There are 0 repository under arabidopsis topic.

• eFP-Seq_Browser

  BioAnalyticResource / eFP-Seq_Browser

  An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.

  rna-seqrna-seq-mappingbioinformaticswebappdata-visualizationefpbamarabidopsisalternative-splicingarabidopsis-thalianadatabase
  Language:HTML 12

• Gregor-Mendel-Institute / SNPmatch

  A simple python library to identify the most likely strain from the population

  genotypesnpsaragenogenotyping-by-sequencinggenotyping1001genomesarabidopsispipelinesnpmatch
  Language:Python 9
• spiro

  jonasoh / spiro

  SPIRO is a Smart Plate Imaging Robot

  arabidopsisbiological-imagingbiologymicrobiologyopen-hardwareplant-scienceraspberry-piscience
  Language:Python 7

• zouyinstein / hifisr

  HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high-fidelity (HiFi) reads or Circular Consensus Sequencing (ccs) data, to a reference genome (i.e., the hypothetical master cycle DNA).

  arabidopsismitochondrial-variantssequencing
  Language:Python 5
• ePlant_Plant_eFP

  BioAnalyticResource / ePlant_Plant_eFP

  A data visualization tool to display tissue expression data for Arabidopsis thaliana

  datadata-visualizationarabidopsis-thalianabioinformaticsbioinformatics-toolbioinformatics-databioinformatics-visualizationdatabasearabidopsis
  Language:JavaScript 3

• Ingefast / small_RNA_analyser

  A pipeline to analyse small RNA expression using Illumina sequencing data

  genomicsarabidopsissmall-rnabioinformatics
  Language:R 2
• AA-GenomicPrediction

  mishaploid / AA-GenomicPrediction

  Genomic prediction of amino acid traits in Arabidopsis seeds

  genomic-predictionamino-acidsarabidopsisgenomic-partitioningsnakemakecookiecutter-data-science
  Language:HTML 2

• athieffry / Thieffry_et_al_2022_Plant_Cell

  🌱🧬 Collection of scripts for the paper: "PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave" (The Plant Cell 2022; PMID 35404429 🔗)

  analysesarabidopsisimmunityplant
  Language:R 1

• bpucker / At7

  Python scripts related to the At7 sequencing project

  genomicssequencingngsarabidopsisplantscellculture
  Language:Python 1

• gauravcodepro / tairaccession

  tairaccession python package for interaction with tair and analyzing arabidopsis genome.

  annotation-processorannotation-toolarabidopsisbioinformaticsbioinformatics-toolcomparative-analysiscomparative-genomicsgenome-analysisgenome-annotationphytozomeplantgenomesplantgenomicstair3
  Language:Python 1
• EcoGEx

  sk-sahu / EcoGEx

  Arabidopsis EcoGEx (R-📦 + 🕸️-App)

  r-packagerpackageshiny-appshinyapprarabidopsisgene-expressiongene-expression-profiles
  Language:R 1

• Sweekwang / golabel

  A website to explore biological relationships between Arabidopsis thailiana genetic characteristics.

  biologicalgotermarabidopsisarabidopsis-thalianageneticsfeature-importance
  Language:JavaScript 1

• Tomas-P / Luciferase-pipeline

  An automated pipeline for analyzing arabidopsis luciferase imaging data

  luciferasearabidopsis
  Language:Python 1
• Thieffry_et_al_2020_Plant_Cell

  athieffry / Thieffry_et_al_2020_Plant_Cell

  🌱🧬 Collection of scripts for the paper: 📑 "Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways" (The Plant Cell 2020; PMID 32213639 🔗)

  arabidopsistranscriptomicsanalysesplant
  Language:R 0

• hagax8 / arabidopsis_viz

  Clustering of 1,135 Arabidopsis thaliana genomes from 1001 Genomes Project (https://1001genomes.org/)

  clusteringgtmancestryarabidopsis1001genomest-sne
  Language:HTML 0

• lmuenter / org.At.tair.db

  Regularly updated version of `org.At.tair.db`.

  arabidopsisgo-termsannotation
  Language:R 0

• rbpisupati / nf-snpmatch

  Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)

  nextflowsnpmatcharagenogenotyping-by-sequencingarabidopsis1001genomes
  Language:Nextflow 0

• Renee-Napoliello / Transcriptomic-Analysis-Arabidopsis-MPBF1c-Knockout

  Analysis of transcriptomic dataset of A. thaliana Multi Protein Bridging Factor 1c knockout

  pythonpython3jupyter-notebookjupyterbioinformaticstranscriptomicsarabidopsisarabidopsis-thalianatranscriptomic-databioinformatics-analysisbiologysciencescience-research
  Language:Jupyter Notebook 0

• gauravcodepro / arabidopsis-api-tair

  easing your access to arabidopsis tair

  annotation-processingannotation-processorannotationsarabidopsisarabidopsis-thalianagenome-analysisgenome-assemblytairtair3
  Language:Python

• gauravcodepro / arabidopsis-maf-cap-accessions

  arabidopsis-maf-cap-accessions. genome extraction, alignments, visualization, phylogenomics, ancestral tree

  arabidopsisarabidopsis-thalianamafphylogenyphylogeny-plotsvisualization
  Language:HTML

• nschan / nf-arassembly

  Nextflow pipeline to assemble genomes from nanopore reads.

  annotationarabidopsisarabidopsis-thalianagenomenanoporenextflowscaffoldinggenome-assemblygenome-sequencingnextflow-pipelinenextflow-pipelines
  Language:Nextflow

• seb-mueller / small-RNA_SWR1

  Anlysis of small RNAs in Arabidopsis SWR1 mutant (published in Choi et al. 2016, Plant Physiology, http://www.plantphysiol.org/content/171/2/1128)

  bioinformaticsrarabidopsispublication-codemicrornaepigenetics

• sivkri / gene-id-retrieval-from-TAIR

  Gene ID Retrieval from TAIR: R code to retrieve gene IDs from TAIR (The Arabidopsis Information Resource) and export them as CSV files

  tairarabidopsisarabidopsis-thalianadata-processingdata-processing-analyticsgene-ids
  Language:R

• tair / ifad-backend

  Interactive Functional Annotations Dashboard

  arabidopsisgeneontologytypescript
  Language:TypeScript