Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by Adamtaranto
A curated list of projects in awesome lists by Adamtaranto .
https://github.com/adamtaranto/teloclip
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
bioinformatics genome-assembly telomere telomere-length telomeres telomeric
Last synced: 27 Oct 2024
https://github.com/adamtaranto/trf2gff
Convert Tandem Repeat Finder dat file output into gff3 format
Last synced: 12 Oct 2024
https://github.com/adamtaranto/blast-besties
Rapid discovery of reciprocal best blast pairs.
Last synced: 12 Oct 2024
https://github.com/adamtaranto/corset-tools
Companion scripts for annotation of Corset generated transcript clusters.
Last synced: 12 Oct 2024
https://github.com/adamtaranto/tirmite
Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
Last synced: 28 Oct 2024
https://github.com/adamtaranto/mite_hunter_2
Minor edits to allow MITE_Hunter (Han & Wessler 2010) to use modern blast+
Last synced: 21 Nov 2024
https://github.com/adamtaranto/ltr-harvest-reformat
Correct sequence names in LTR_Harvest GFF3 output.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/frisk
Screen genomic scaffolds for regions of unusual k-mer composition.
Last synced: 12 Oct 2024
https://github.com/adamtaranto/density-mapr
An R workflow for creating heat-maps representing the spatial association between two genomic feature sets
Last synced: 21 Nov 2024
https://github.com/adamtaranto/mimeo
Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/yanagiba
Filter and slice Nanopore reads which have been basecalled with Albacore.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/subset-fasta-by-name
Subset, split, and correct formatting of multiple sequence FASTA files.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/te-insertion-scanner
Scan whole genome alignments for signatures of transposon insertion.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/te-splitter
Extract terminal repeats from retrotransposons (LTRs) or DNA transposons (TIRs). Compose synthetic MITES from complete DNA transposons.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/te-dispersion-metric
Proposed metric for measuring the clustering of transposons within a genome
Last synced: 21 Nov 2024
https://github.com/adamtaranto/howtoscience
A knowledge engine for new students of bioinformatics.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/gi2descript
Fetch summary data from NCBI for genbank records using GI numbers
Last synced: 21 Nov 2024
https://github.com/adamtaranto/derip2
Predict progenitor sequence of fungal repeat families by correcting for RIP-like mutations and cytosine deamination events. Mask RIP or deamination events from alignments.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/planets
Example git repo for wehi git intro course.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/transposon-tools-list
A list of useful software tools for predicting, classifying, annotating, and analysing Transposable Elements.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/catcount
Concatenate count tables for RNA-seq reads mapped to features by htseq-count
Last synced: 21 Nov 2024
https://github.com/adamtaranto/quick-ortho-fetch
Take an XML formatted multiblast result, extract genbank IDs for best x hits to each query and download a non-redundant list of matching seqs from ncbi.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/low-mem-genomics
Low memory methods for genomic software development
Last synced: 21 Nov 2024
https://github.com/adamtaranto/nbgrader-gitpod-template
Config scripts for managing nbgrader envs in Gitpod
Last synced: 21 Nov 2024
https://github.com/adamtaranto/methfreq
Calculate observed vs expected instances of DNA-methylation motifs in gene sequences
Last synced: 21 Nov 2024
https://github.com/adamtaranto/git-workshop-aug
Intro to git unimelb Aug 2024
Last synced: 21 Nov 2024
https://github.com/adamtaranto/te-annotation-workflow
Workflow and useful tools for annotating transposable elements in sequenced genomes
Last synced: 21 Nov 2024
https://github.com/adamtaranto/te-reunite
For a set of reference transposons, collect instances from one or more genomes. Use aligned collections to build models capturing TE family diversity or produce deRIP'd reference sequence.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/nearestfeat
Fork of nearestfeat, a tool for calculating distance between members of feature classes in a GFF annotation. Migrating to Python3
Last synced: 21 Nov 2024
https://github.com/adamtaranto/reconcile
Take clustered element fragment coordinates from RECON and write sequences to fasta for alignment and consensus calling.
Last synced: 21 Nov 2024
https://github.com/adamtaranto/student-gitpod-template
A template repo for students to work on coding workshops in Gitpodpod Workspace with Conda package management..
Last synced: 21 Nov 2024
https://github.com/adamtaranto/python-novice-dataframes
Working with tabular data in Python
Last synced: 21 Nov 2024
https://github.com/adamtaranto/graphtagger
Small script to compute coverage of contigs from reads
Last synced: 21 Nov 2024
https://github.com/adamtaranto/promer2circos
Takes promer sequence matches formatted with show_coords, and reformats for use as a circos linkage track
Last synced: 21 Nov 2024
https://github.com/adamtaranto/learn-hatch
Learning how to do python packaging with Hatch.
Last synced: 20 Nov 2024