UCSF Francis Lab

This needs a bit of cleanup and organization.

Pseudo Pipeline and Topic Notes

• Current
  • AWS
  • C4
  • UCSF
  • Cutadapt
  • Bowtie2
  • AlphaFold
  • Foldseek
  • PhIPseq / Phage Display
  • TEProF2
  • Singularity
  • MHC

• ---

• Archive
  • MHC
  • AlphaFold
  • EV
  • Demultiplex
  • Preprocessing
  • DNASeq
  • RNASeq
  • RNAStrandedness
  • miRNA
  • APOBEC
  • Aligners
    • Bowtie2
    • Bowtie
    • BWA
    • STAR
    • Blat
    • Blast
    • Diamond
    • Kraken
    • Kallisto
    • Salmon
    • Foldseek
  • VCF
  • K-mer Analysis
    • iMOKA
    • GECKO
    • HAWK
    • MetaGO
  • Repeat / Transposable Elements
    • MELT
    • REdiscoverTE
    • TEfinder
    • xTea
    • GeneTEFlow
    • SQuIRE
    • RepEnrich2
    • TEtools
    • McClintock
    • TEtranscripts
    • TEProF2
• Computing Resources, Cloud Services and Data Sources
  • General Cloud
  • C4
  • TIPCC
  • AWS
  • eRA Commons
  • ENA European Nucleotide Archive
  • UK BioBank RAP
  • SGDP
  • CGC
  • St Jude
  • LatchBio
  • Use Galaxy
  • TCGA
  • TARGET
  • GTEx
  • dbGaP
  • Seven Bridges
  • 1000 Genomes
• Assemblers
• Box
• Catchitt
• Chimera
• CIRCexplorer2
• Cutadapt
• Dark
• DESeq
• DiscordRetro
• ERVCaller
• Features
• GWAS
• GuideSeq
• hervQuant
• HLA
• Illumina
• Imputation
• KMC
• Long Read / ONT
• Manta_Strelka
• Masking
• PhIPseq / Phage Display
• References
• Sleuth
• SNP2HLA
• Taxonomy
• TelSeq
• TensorFlow
• UMI
• Notebooks
  • Jupyter
  • Rmarkdown
• Tools
  • Singularity
  • Docker

General

• UCSF Github Repos
• UNR Github Repos
• Cal Github Repos
• Jake's Github Repos

Helpful links

• C4 - Research Computing at Scale
• TIPCC - a High-Performance Compute Environment at UCSF
• Wynton HPC
• AWS Cloud Credits for Research
• Github Pages