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discasm
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public |
DISCASM aims to extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads. DISCASM relies on the output from STAR (as run via STAR-Fusion), and supports de novo transcriptome assembly using Trinity or Oases. - https://github.com/DISCASM/DISCASM/wiki
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2025-04-22 |
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loompy
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public |
Work with .loom files for single-cell RNA-seq data
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2025-04-22 |
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backspinpy
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public |
backSPIN clustering algorythm
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2025-04-22 |
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r-phangorn
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public |
Package contains methods for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.
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2025-04-22 |
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lorma
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public |
LoRMA is a tool for correcting sequencing errors in long reads.
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2025-04-22 |
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ssu-align
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public |
SSU-ALIGN: structural alignment of SSU rRNA sequences
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2025-04-22 |
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binsanity
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public |
Method to cluster contigs based a biphasic method with coverage and composition
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2025-04-22 |
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curlywhirly
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public |
CurlyWhirly is an application for viewing multi-dimensional data, with a particular focus on the outputs of Principle Coordinate Analysis and Principal Components Analysis
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2025-04-22 |
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barrnap-python
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public |
python package for Torsten Seemann's barrnap package for annotating rRNAs
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2025-04-22 |
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bioconductor-chimeraviz
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public |
Visualization tools for gene fusions
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2025-04-22 |
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r-argumentcheck
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public |
The typical process of checking arguments in functions is iterative. In this process, an error may be returned and the user may fix it only to receive another error on a different argument. 'ArgumentCheck' facilitates a more helpful way to perform argument checks allowing the programmer to run all of the checks and then return all of the errors and warnings in a single message.
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2025-04-22 |
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sprai
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public |
Sprai (single-pass read accuracy improver) is a tool to correct sequencing errors in single-pass reads for de novo assembly. It is originally designed for correcting sequencing errors in single-molecule DNA sequencing reads, especially in Continuous Long Reads (CLRs) generated by PacBio RS sequencers. The goal of Sprai is not maximizing the accuracy of error-corrected reads; instead, Sprai aims at maximizing the continuity (i.e., N50 contig length) of assembled contigs after error correction.
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2025-04-22 |
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tirmite
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public |
Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
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2025-04-22 |
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tinscan
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public |
Find alignment signatures characteristic of transposon insertion sites.
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2025-04-22 |
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mimeo
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public |
Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.
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2025-04-22 |
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flapjack
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public |
Flapjack provides interactive visualizations of high-throughput genotyping data.
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2025-04-22 |
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tablet
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public |
Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
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2025-04-22 |
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dupre
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public |
Duplicate rate estimation using linear programming and the hypergeometric distribution
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2025-04-22 |
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dialign-tx
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public |
DIALIGN-TX is a greedy and progressive approaches for segment-based multiple sequence alignment
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2025-04-22 |
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biskit
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public |
A Python platform for structural bioinformatics.
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2025-04-22 |
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galaxy-ie-helpers
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public |
Helper scripts to work with Galaxy's Interactive Environments
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2025-04-22 |
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galaxy-parsec
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public |
Command-line utilities to assist in interacting with Galaxy servers (http://galaxyproject.org/).
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2025-04-22 |
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justbackoff
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public |
Simple backoff algorithm in Python
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2025-04-22 |
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pyimzml
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public |
Parser for conversion of imzML 1.1.0 files
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2025-04-22 |
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pyimagingmspec
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public |
Python library for processing imaging mass spectrometry data
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2025-04-22 |
