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slncky
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public |
slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution. slncky was developed as a collaboration between the Garber Lab at UMass Medical and the Regev Lab at the Broad Institute.
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2025-04-22 |
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allegro
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public |
A fast linkage and haplotype analysis utility making use of MTBDD to reduce complexity.
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2025-04-22 |
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gdc-client
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public |
GDC Data Transfer Tool
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2025-04-22 |
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swiftlink
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public |
A multipoint parametric linkage analysis tool for large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees.
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2025-04-22 |
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menetools
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public |
Python 3 Metabolic Network Topology Tools
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2025-04-22 |
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ideas
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public |
A method for jointly and quantitatively characterizing multivariate epigenetic landscapes in many cell types, tissues or conditions.
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2025-04-22 |
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bioconductor-fgsea
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public |
Fast Gene Set Enrichment Analysis
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2025-04-22 |
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meraculous
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public |
Meraculous is a whole genome assembler for Next Generation Sequencing data, geared for large genomes. It's hybrid k-mer/read-based approach capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on a high-cpu cluster in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.
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2025-04-22 |
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feht
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public |
A commandline program to automatically identify markers predictive of groups. Can be used with binary data, genomic (single nucleotide variant) data, or arbitrary character data.
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2025-04-22 |
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simwalk2
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public |
Stochastic Statistical Analysis of Qualitative Traits
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2025-04-22 |
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pyasp
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public |
A convenience wrapper for the ASP tools gringo, gringo4 and clasp.
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2025-04-22 |
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tqdist
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public |
computes the triplet distance between rooted trees in O(n log n) time and the quartet distance between unrooted trees in O(dn log n) time, where d degree of the tree with the smallest degree.
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2025-04-22 |
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ghm
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public |
A MOD-score analysis in which parametric LOD scores are maximized over the parameters of the trait model
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2025-04-22 |
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lordec
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public |
A hybrid error correction program for long, PacBio reads
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2025-04-22 |
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prestor
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public |
A prototype package for generating quality control plots from pRESTO output.
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2025-04-22 |
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r-alakazam
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public |
Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
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2025-04-22 |
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cassiopee
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public |
scan an input genomic sequence (dna/rna/protein) and search for a subsequence with exact match or allowing substitutions (Hamming distance) and/or insertion/deletions
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2025-04-22 |
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sift4g
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public |
SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms.
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2025-04-22 |
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rad_haplotyper
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public |
A program for building SNP haplotypes from RAD sequencing data
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2025-04-22 |
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commet
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public |
Comparing and combining multiple metagenomic datasets
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2025-04-22 |
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yanagiba
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public |
Filter short or low quality Oxford Nanopore reads which have been basecalled with Albacore.
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2025-04-22 |
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bioconductor-hicrep
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public |
Measuring the reproducibility of Hi-C data
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2025-04-22 |
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takeabreak
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public |
tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes
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2025-04-22 |
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nanolyse
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public |
Removing lambda DNA control reads from fastq dataset
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2025-04-22 |
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tantan
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public |
tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences.
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2025-04-22 |
