peterdfields's repositories
Angst_etal_2022_MolEcol
Scripts used in Angst et al. (2022)
3DFI
The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.
Angst_etal_2023_G3
Scripts used in Angst et al. (2023)
arabidopsis_numt-1
Analysis of Arabidopsis thaliana Chromosome 2 numt
Bash-Oneliner
A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.
Col-CEN
Resources for the Col-CEN reference genome assemblies
cs-nf-pipelines
The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines
deepconsensus
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
DeepMod2
DeepMod that works on Guppy or Tombo generated FAST5 files
foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
gpn
Genomic Pre-trained Network
graph_peak_caller
ChIP-seq peak caller for reads mapped to a graph-based reference genome
grenedalf
Toolkit for Analyzing Allele Frequencies of Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
latex-nihbiosketch
A LaTeX class implementing the new NIH Biographical Sketch Format
locator
deep learning prediction of geographic location from individual genome sequences
redmask
Genome assembly soft-masking using Red (REpeat Detector)
rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments, including variant calling and more - relating to population genetics and insecticide resistance
TransPi
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly