Reverse Dependencies of pysam
The following projects have a declared dependency on pysam:
- iCallSV — The module helps to call structural variants using NGS data set on human.
- igv-reports — Creates self-contained html pages for visual variant review with IGV (igv.js).
- ilmn-pelops — Dedicated caller for DUX4 rearrangements from whole genome sequencing data.
- imfusion — Tool for identifying transposon insertions in Insertional Mutagenesis screens from gene-transposon fusions using single- and paired-end RNA-sequencing data.
- ImputeHiFI — no summary
- indelpost — Python library for simple and complex indels
- index-bam-by-read-id — Sort, index and search BAM files by read ID
- indextools — A toolkit for accelerating genomics using index files.
- ingenannot — InGenAnnot: Inspection of Gene Annotation
- InSilicoSeq — a sequencing simulator
- insilicosv — Simulator of complex structural variants in genomes
- intron — Intron retention tool
- iqkm — Identification and quantification of KEGG Modules in metagenomes/genomes
- irescue — Interspersed Repeats singl-cell quantifier
- iScanVCFMerge — Python tool to merge cross-species Illumina iScan genotype data with a reference set of genotypes from a pre-existing source.
- iscard — simple CNV caller for NGS
- iseq-prof — ISEQ profiling
- isocomp — no summary
- IsoCon — Pipeline for obtaining non-redundant haplotype specific transcript isoforms using PacBio IsoSeq reads.
- isONclust — De novo clustering of long-read transcriptome reads.
- isotools — Framework for the analysis of long read transcriptome sequencing data
- isovar — Determine mutant protein sequences from RN using assembly around variants
- janggu — Utilities and datasets for deep learning in genomics
- JKBio — A useful module for any CompBio
- jla-tailer — Tool to find 3' tailing of non-coding RNAs
- karyoplot — karyoplot: annotations along the genome
- Katana — Command-line tool to soft-clip reads based on primer locations.
- kerasAC — keras Accessibility Models (kerasAC)
- kipoi_veff — kipoi_veff: variant effect prediction plugin for Kipoi
- krisp — A lightweight tool for finding diagnostic regions in whole genome data
- labw-utils — Utilities Python functions & classes used in LabW
- LAFITE — Nanopore Direct RNA-seq Transcriptome Assembly
- lakeview — A Python library for creating publication-quality genome visualisations.
- leukgen-disambiguate — Disambiguate reads mapping to multiple genomes. This is a frozen release with some bug fixes of the original AstraZeneca-NGS/disambiguate v1.0.
- lifesci — This repo contains python3 life sciences utilities.
- Liftoff — A gene annotation mapping tool
- lifton — Combining DNA and protein alignments to improve genome annotation with LiftOn
- liftover-bam — A simple module to liftover bam alignments
- liqa — A statistical tool to quantify isoform-specific expression using long-read RNA-seq
- LRphase — Phasing individual long reads using known haplotype information.
- machado — This library provides users with a framework to store, search and visualize biological data.
- MAGOT2 — "New, simpler toolkit for random common genomic analyses"
- make-bitvector — Create bitvectors for DMS seq data
- mapping-length-analysis — Analyse number of raw and mapped reads by length
- marker-alignments — Process and summarise alignments of metagenomic sequencing reads to reference databases of marker genes
- maskara — maskara
- maslongbow — Annotation and segmentation of MAS-seq data
- MATES — no summary
- mavis — A Structural Variant Post-Processing Package
- mbf-align — Alignment of high througput sequencing data
- mbf-genomes — wrappers for external algorithms
- mbf-genomics — All about intervals on genomic data
- mclumi — UMI de-duplication using mclUMI
- mdu-snpit — MDU snpit
- megalodon — Nanopore base calling augmentation
- megrim — A bioinformatics tutorial framework for epi2me-labs
- mendelmd — no summary
- mergesvvcf — Merge SV VCF calls. Fork of https://github.com/ljdursi/mergevcf by Jonathan Dursi (Jonathan.Dursi@oicr.on.ca)
- MetaPhlAn — MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
- metator — A pipeline for binning metagenomic datasets from metaHiC data.
- methtuple — methtuple
- methylartist — Tools for parsing and plotting nanopore methylation data
- methylbert — A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution
- methylink — methylink is a tool to link methylation tags between SAM/BAM files.
- mgefinder — A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
- mgkit — Metagenomics Framework
- mgnifyextract — This library extracts Darwin Core datasets from MGnify
- midas2 — https://midas2.readthedocs.io/en/latest/
- mim-seq — Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
- mimseq — Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
- minion-data — no summary
- mip2scout — Microservice :)
- MIRACLEpy — Microsatellite Instability (MSI) detection with RNA sequencing data.
- MisER — Find and fix missed small exons.
- MisSER — Find and fix missed small exons.
- mitoviz — Plot variants on the human mitochondrial genome.
- mitty — Simulator for genomic data
- mitywgs — A sensitive Mitochondrial variant detection pipeline from WGS data
- mobidic-mpa — MPA: MoBiDiC Prioritization Algorithm
- modbamtools — A set of tools to manipulate and visualize data from base modification bam files
- modbedtools — Generate modbed track files for visualization on WashU Epigenome Browser
- modulename — this is a description
- morinkit — Python functions for cancer genomics
- MotifDiff-pkg — no summary
- muon — Multimodal omics analysis framework
- mutacc — The mutation accumulation database
- mutanno — Mutation Annotation Tool
- mutract — Extracting single cell variants from bam file
- mutview — A command tool to view reads over a loci from bam file, like a lightweigth IGV
- NanoCount — EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
- nanome-jax — NANOME (Nanopore methylation) pipeline developed by Li Lab at The Jackson Laboratory
- nanomethphase — Phase long reads from Oxford Nanopore Technologies based on their methylated profile.
- ness-search — NESS: Vector-based Alignment-free Sequence Search
- ngs-test-utils — Utilities for generation of synthetic NGS files
- ngs-toolkit — A toolkit for NGS analysis with Python.
- ngsci — The Next Generation Sequencing Complexity Index
- ngsderive — Forensic analysis tool useful in backwards computing information from next-generation sequencing data.
- ngsfragments — Python package for Next Generation Sequencing fragment manipulation
- ngsscriptlibrary — Scripts for NGS data-analysis
- ngstoolkits — ngstools