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Package Name Access Summary Updated
ucsc-hgloadout public load RepeatMasker .out files into database 2024-12-12
r-biodb public An R package for connecting to chemical and biological databases. 2024-12-12
gffcompare public GffCompare by Geo Pertea 2024-12-12
boutroslabplottinggeneral public No Summary 2024-12-12
ucsc-fastqtofa public Convert from fastq to fasta format. 2024-12-12
miniasm public Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2024-12-12
ucsc-hgloadmaf public Load a maf file index into the database 2024-12-12
ucsc-mafaddqrows public Add quality data to a maf 2024-12-12
ucsc-mafsinregion public Extract MAFS in a genomic region 2024-12-12
ucsc-farc public Reverse complement a FA file 2024-12-12
ucsc-maftosnpbed public finds SNPs in MAF and builds a bed with their functional consequence 2024-12-12
ucsc-maskoutfa public Produce a masked .fa file given an unmasked .fa and 2024-12-12
ucsc-gff3topsl public convert a GFF3 CIGAR file to a PSL file 2024-12-12
links public Long Interval Nucleotide K-mer Scaffolder 2024-12-12
daligner public DALIGNER: Find all significant local alignments between reads 2024-12-12
blockbuster public Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. 2024-12-12
regtools public Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. 2024-12-12
ucsc-transmappsltogenepred public convert PSL alignments of mRNAs to gene annotations. 2024-12-12
wtdbg public Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly 2024-12-12
survivor public Toolset for SV simulation, comparison and filtering 2024-12-12
netcdf-metadata-info public Metadata information from netcdf file for Galaxy use. 2024-12-12
bwa public The BWA read mapper. 2024-12-12
fermi public A WGS de novo assembler based on the FMD-index for large genomes 2024-12-12
cmph public No Summary 2024-12-12
merfishtools public MERFISHtools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data. On top, differential expression analysis can be performed for two or multiple conditions, including credible intervals for fold change and coefficient of variation, and controlling the expected false discovery rate. 2024-12-12
bgt public Flexible genotype query among 30,000+ samples whole-genome. 2024-12-12
ucsc-bigmaftomaf public convert bigMaf to maf file 2024-12-12
ucsc-bigbednameditems public Extract item of given name from bigBed 2024-12-12
conus public CONUS is an implementation of simple stochastic context-free grammars for RNA secondary structure analysis.CONUS developed for exploring the consequences of different single sequence SCFG designs in predicting RNA secondary structure. 2024-12-12
dazz_db public DAZZ_DB: The Dazzler Data Base 2024-12-12
ucsc-bigwiginfo public Print out information about bigWig file. 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
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
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