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Package Name Access Summary Updated
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
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
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
r-mcpcounter public Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression 2024-12-12
ucsc-xmltosql public Convert XML dump into a fairly normalized relational database 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
iqtree public Efficient phylogenomic software by maximum likelihood. 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
ucsc-mafsplitpos public Pick positions to split multiple alignment input files 2024-12-12
r-rrbgen public A lightweight limited functionality R bgen read/write library 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
fastahack public No Summary 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
ucsc-nettobed public Convert target coverage of net to a bed file. 2024-12-12
tn93 public This is a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance. 2024-12-12
sambamba public Tools for working with SAM/BAM data 2024-12-12
migraine public Implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently  handled are allelic counts but sequences will be handled in the forthcoming version. 2024-12-12
bowtie2 public A fast and sensitive gapped read aligner. 2024-12-12
libbambamc public No Summary 2024-12-12
rnasnp public No Summary 2024-12-12
novoalign public Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms 2024-12-12
ucsc-nettoaxt public Convert net (and chain) to axt. 2024-12-12
faqcs public Quality Control of Next Generation Sequencing Data. 2024-12-12
muse public An accurate and ultra-fast somatic point mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples. 2024-12-12
ucsc-bedclip public Remove lines from bed file that refer to off-chromosome locations. 2024-12-12
ucsc-toupper public Convert lower case to upper case in file. Leave other chars alone 2024-12-12
ucsc-hgloadwiggle public Load a wiggle track definition into database 2024-12-12
smartdenovo public Ultra-fast de novo assembler using long noisy reads 2024-12-12
ucsc-headrest public Return all *but* the first N lines of a file. 2024-12-12
dnp-binstrings public Convert fasta strings into dinucleotide binary indicator string as 00101... 2024-12-12
ucsc-mafranges public Extract ranges of target (or query) coverage from maf and 2024-12-12
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