Pinned Repositories
16S_Tutorial
2014-5-metagenomics-workshop
Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm
2016
Materials prepared by the instructors of the #NGSchool2016
2016-tutorials
repo for 2016 EDAMAME tutorials
2017
Materials used during #NGSchool2017
AliTV
Visualize whole genome alignments as linear maps
angus
Materials for Analyzing Next-Generation Sequencing (ANGUS) course.
Annocript
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript
apt-cyg
Apt-cyg, an apt-get like tool for Cygwin
LS-BSR
Large scale Blast Score Ratio (BSR) analysis
palc's Repositories
palc/16S_Tutorial
palc/AliTV
Visualize whole genome alignments as linear maps
palc/Annocript
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript
palc/apt-cyg
Apt-cyg, an apt-get like tool for Cygwin
palc/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
palc/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
palc/Filtlong
quality filtering tool for long reads
palc/FMAP
Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
palc/genome_scripts
collection of random scripts for processing genome related files. the shell scripts are specific to my environment and may not work elsewhere.
palc/getSeqENA
Get fastq files from ENA using Run IDs
palc/graphmap
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html
palc/hap.py
Haplotype VCF comparison tools
palc/hh-suite
Remote protein homology detection suite.
palc/HmmUFOtu
An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing
palc/Metatranscriptome-Workshop
Metatranscriptomics Tutorial
palc/MetaViC
Virus metagenomics pipeline for unknown host or in absence of a host genome
palc/MicrobialGenomicsScripts
A selection of short scripts for analyzing microbial genomes
palc/minion_multiQC
multi-tool QC for minion data
palc/neatseq-flow-modules
Shared Modules and Workflows for NeatSeq-Flow
palc/phytophthora
Scripts used in the analysis of Phytophthora genomes
palc/phytophthora_fragariae
Commands used in the analysis of P. fragariae genomes
palc/plotly
An interactive graphing library for R
palc/prokaryote_RNASeq
introduction to analysis of prokaryote RNASeq data with an associated reference genome
palc/RStartHere
A guide to some of the most useful R Packages that we know about
palc/RVDB
A reference viral database (RVDB)
palc/toast2018
Introduction to Nanopore Sequencing - Prac material and presentations from The Omics Australia Tutorials Sydney (TOAST) workshop 19th - 20th of March 2018.
palc/tutorials-1
Tutorials on phylogenetic and phylogenomic methods
palc/tutorials-2
:books: Various bioinformatics tutorials
palc/vr-codebase
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
palc/world-map-r
A simple script to display stuff on a world map with R and ggplot