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sci-biology/Fastaq

Manipulate FASTA/Q, GFF3, EMBL, GBK files with API for developers

sci-biology/ONTO-PERL

Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)

sci-biology/SPAdes

De novo de Bruijn genome assembler overcoming uneven coverage

sci-biology/afni

Analysis of Functional Neuroimages by NIMH

sci-biology/assembly-stats

Assembly statistics (min, max, sum, N50, N90, count gaps and Ns)

sci-biology/bam-readcount

Count DNA sequence reads in BAM files and other statistics calculations

sci-biology/bambus

Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle

sci-biology/barrnap

Predict Bacterial and Archaeal rRNA genes and output in GFF3 format

sci-biology/brkraw

Fast and easy statistical learning on NeuroImaging data

sci-biology/bx-python

Library for rapid implementation of genome scale analyses

sci-biology/cutadapt

Adapter trimming and other preprocessing of high-throughput sequencing reads

sci-biology/dcm2niix

DICOM to NIfTI converter

sci-biology/dcmstack

DICOM to Nifti coversion

sci-biology/deeptools-intervals

Constructing interval trees with associated exon/annotation information

sci-biology/deeptools

Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig

sci-biology/diamond

Alternative of blastp/blastx searches using DNA short reads through protein db

sci-biology/flexbar

Barcode, MID tag and adapter sequence removal

sci-biology/dipy

Computational neuroanatomy project focusing on diffusion MRI

sci-biology/freebayes

Bayesian gen. variant detector to find short polymorphisms

sci-biology/glean

Merge various gene prediction into one (unsupervised learning system)

sci-biology/genepop

Population genetics analysis

sci-biology/gffutils

GFF and GTF file manipulation and interconversion

sci-biology/graf-bin

Find closely related subjects using SNP genotype data, validate pedigree file

sci-biology/hisat2

Align DNA reads to a population of genomes

sci-biology/jtreeview-bin

Viewer for Microarray Data in PCL or CDT formats

sci-biology/mappy

Minimap2 python binding

sci-biology/mmseqs2

Fast and sensitive sequence search and clustering

sci-biology/megahit

Metagenome assembler using succinct de Bruijn graph approach with CUDA

sci-biology/minimap2

splice-aware sequence aligner with SSE2 and SSE4.1

sci-biology/multiqc

Aggregate bioinformatics results across many samples into a single report

sci-biology/open-ephys-gui

Processing, recording, and visualizing multichannel ephys data

sci-biology/nitime

Time-series analysis of neuroscience data

sci-biology/pbbam

PacBio modified BAM file format

sci-biology/pbcopper

Core C++ library for data structures, algorithms, and utilities

sci-biology/roiextractors

Optical imaging data handling from several file formats

sci-biology/stacks

Analyze restriction enzyme data, draw gen. maps, population genomics

sci-biology/swissknife

Perl library of modules to manipulate SwissProt flatfiles

sci-biology/trinityrnaseq

Transcriptome assembler for RNA-seq reads

sci-biology/vcflib

VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)

sci-biology/twinscan

iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. pipeline

sci-chemistry/MotionCor2

Correction of electron beam-induced sample motion

sci-chemistry/nmrpipe

Spectral visualisation, analysis and Fourier processing

sci-chemistry/concoord

Protein conformations around a known structure based on geometric restrictions

sci-chemistry/pales-bin

Prediction of alignment from structure

sci-chemistry/ssp

Secondary structure propensities

sci-chemistry/mics

Prediction of Protein Structural Motifs from NMR Chemical Shifts

sci-chemistry/panav

Probabilistic approach for validating protein NMR chemical shift assignments

sci-chemistry/chimera

Next generation molecular visualization program from RBVI

sci-chemistry/drawxtl

Crystal structure drawings from structural data

sci-chemistry/ctffind

CTF estimation (ctffind, ctftilt)