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Package Name Access Summary Updated
ucsc-bigwiginfo public Print out information about bigWig file. 2024-12-12
get_fasta_info public get_FAST{A,Q}_info - Get fast info on fasta and fastq files 2024-12-12
simwalk2 public Stochastic Statistical Analysis of Qualitative Traits 2024-12-12
fastq-multx public Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not. 2024-12-12
ucsc-bedsort public Sort a .bed file by chrom,chromStart 2024-12-12
r-buencolors public R utility package for color mapping and plot aesthetics. 2024-12-12
ucsc-rowstocols public Convert rows to columns and vice versa in a text file. 2024-12-12
r-sbpiper public Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation 'sbpiper' calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation 'sbpiper' calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software 'SBpipe'. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>. 2024-12-12
cyntenator public progressive gene order alignments 2024-12-12
cmaple public MAximum Parsimonious Likelihood Estimation in C/C++. 2024-12-12
cesar public CESAR 2.0 is a method to realign coding exons or genes to DNA sequences using a Hidden Markov Model 2024-12-12
ucsc-overlapselect public Select records based on overlapping chromosome ranges. The ranges are specified in the selectFile, with each block specifying a range. Records are copied from the inFile to outFile based on the selection criteria. Selection is based on blocks or exons rather than entire range. 2024-12-12
ucsc-spacedtotab public Convert fixed width space separated fields to tab separated 2024-12-12
ema public Fast & accurate alignment of barcoded short-reads 2024-12-12
dwgsim public Whole Genome Simulator for Next-Generation Sequencing 2024-12-12
fastq-count public Simple fastq read and base counter for paired data. 2024-12-12
msaprobs public MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. 2024-12-12
r-mcpcounter public Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression 2024-12-12
fastq-pair public fastq-pair: efficient synchronization of paired-end fastq files 2024-12-12
ucsc-xmltosql public Convert XML dump into a fairly normalized relational database 2024-12-12
dligand2 public DLIGAND2 is a knowledge-based method to predict protein-ligand binding affinity based on a distance-scaled, finite, ideal-gas reference (DFIRE) state. 2024-12-12
ucsc-pslfilter public filter out psl file 2024-12-12
salmon public Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment 2024-12-12
ucsc-fatotwobit public Convert DNA from fasta to 2bit format. 2024-12-12
ucsc-pslreps public Analyze repeats and generate genome-wide best alignments from a 2024-12-12
svmlight public SVMLight Library by Thorsten Joachim 2024-12-12
ucsc-parahubstop public version 12.18 2024-12-12
r-qorts public QoRTs toolkit for analysis, quality control, and data management of RNA-Seq datasets. 2024-12-12
ucsc-genepredtogtf public Convert genePred table or file to gtf. 2024-12-12
ucsc-taillines public add tail to each line of file 2024-12-12
verifyidintensity public verifyIDintensity detects and estimates sample contamination using intensity data from Illumina genotyping arrays. 2024-12-12
ucsc-mafsplitpos public Pick positions to split multiple alignment input files 2024-12-12
peregrine-2021 public A genome assembler designed for long-reads that have good enough accuracy 2024-12-12
r-rrbgen public A lightweight limited functionality R bgen read/write library 2024-12-12
dinamo public An exact and efficient method for IUPAC motif discovery in DNA sequences 2024-12-12
metacache public MetaCache is a classification system for mapping genomic sequences (short reads, long reads, contigs, ...) from metagenomic samples to their most likely taxon of origin. 2024-12-12
ucsc-netchainsubset public Create chain file with subset of chains that appear in the net 2024-12-12
kmergenie public KmerGenie estimates the best k-mer length for genome de novo assembly 2024-12-12
ucsc-bedremoveoverlap public Remove overlapping records from a (sorted) bed file. Gets rid of 2024-12-12
pyspoa public Python binding to spoa library. 2024-12-12
rtk public rtk - rarefaction toolkit for OTU tables 2024-12-12
fastahack public No Summary 2024-12-12
pyabpoa public pyabpoa: SIMD-based partial order alignment using adaptive band 2024-12-12
pear public paired-end read merger 2024-12-12
ucsc-pslstats public collect statistics from a psl file. 2024-12-12
ucsc-netfilter public Filter out parts of net. What passes 2024-12-12
tssar public No Summary 2024-12-12
skesa public Strategic Kmer Extension for Scrupulous Assemblies & Sequence Assembly Using Target Enrichment 2024-12-12
perl-xml-libxslt public Interface to GNOME libxslt library 2024-12-12
poseidon-xerxes public A tool (xerxes) to analyse genotype databases formatted using Poseidon. 2024-12-12
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