Reverse Dependencies of pysam
The following projects have a declared dependency on pysam:
- nucflag — NucFlag misassembly identifier.
- NucleoATAC — python package for calling nucleosomes with ATAC-Seq
- oligo-capture — A tool for designing oligos for DNA capture
- olivar — Olivar pipeline
- omniclip — no summary
- ont-remora — Nanopore methylation/modified base calling detached from basecalling
- PacbioDataProcessing — Tools to process PacBio sequencing data at molecule level
- pairtools — CLI tools to process mapped Hi-C data
- panisa — panISa is a software to search insertion sequence (IS) on resequencing data (bam file)
- panpipes — Panpipes - multimodal single cell pipelines
- paraphase — paraphase: HiFi-based caller for highly homologous genes
- parse-vcf — Variant Call Format parser and convenience methods
- pbiotools — Miscellaneous bioinformatics and other supporting utilities for Python 3
- peakqc — Module for quality control of ATAC-seq data
- peaks2utr — A robust, parallelized Python CLI for annotating three_prime_UTR
- PEALS — Peak-based Enhancement Analysis PipeLine for MeRIP-seq
- pebbles — A package for calling HGVS variants in single SAM/BAM alignments
- pepper-polish — RNN based standalone assembly polisher.
- phantombuster — no summary
- PHASEfilter — Software package to filter variants, SNPs and INDELs, that are present in heterozygous form in phased genomes.
- PheWeb — A tool for building PheWAS websites from association files
- pipeclip — PIPELINE FOR CLIP SEQ DATA
- piper — A lightweight python toolkit for gluing together restartable, robust command line pipelines
- plassembler — Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates
- polygenic — Polygenic score toolkit
- PoolSeqProGen — A package for creating variant protein databases for bacteria from Pool-seq experiments
- poreplex — A versatile sequence read processor for nanopore direct RNA sequencing
- probNORM — Method for structural probing signal calculation that eliminates read distribution bias and prevents reactivity underestimation.
- prophyle — ProPhyle metagenomic classifier
- psite — Model-based inference of P-site offsets
- py-popgen — Software platform for facilitating population genomic analyses
- py3helpers — Python utility functions.
- pybcf — Package for loading data from bcf files
- pybio — pybio genomics
- pyBioTools — pyBioTools is a collection of tools to manipulate biological sequences
- pychromvar — A python package for chromVAR
- pycltools — pycltools is a package written in python3 containing a collection of generic functions and classes for file parsing, manipulation...
- pydamage — Damage parameter estimation for ancient DNA
- pydbsnp — Interface with dbSNP VCF data
- pydemux — Python package for demultiplexing raw sequencing reads in SAM/BAM format
- pydownsampler — A Python package for downsampling sequence alignment files
- pyeasyfuse — EasyFuse is a pipeline to detect fusion transcripts from RNA-seq data with high accuracy.
- pygbrowse — Tools for making plots of genomic datasets in a genome-browser-like format
- pyGenomeTracks — Command-line tool to make beautiful and reproducible genome browser snapshots
- pygwasvcf — A package for reading GWAS summary statistics stored in VCF/BCF format
- pyim — Tool for identifying transposon insertions from targeted DNA-sequencing data.
- pyLAD — pyLAD: Python-based DamID Lamina-Associated-Domain analysis
- pyllelic — Analysis of allele-specific methylation in bisulfite DNA sequencing.
- pyNextGen — [UNSTABLE] A package of custom tools to tackle bioinformatic projects.
- pyPINTS — Peak Identifier for Nascent Transcripts Starts (PINTS)
- pyreference — Library for working with reference genomes and gene GTF/GFFs
- pysamiterators — Pysam related iterators
- pySeqRNA — pySeqRNA a python based RNA analysis package
- pysmoove-summary — Summarize pysmoove SV calling VCF results in a BED-like format
- pytest-wdl — Fixtures for pytest for running WDL workflows using Cromwell.
- pyupdog — Python program for calculating UPD
- pyvariantfilter — Python package for filtering variants.
- pyYAMB — Yet Another Metagenome Binner
- RagTag — Fast reference-guided genome assembly scaffolding
- ramifi — Script to do recombinant read analysis
- rase — rase
- RCK — A tool for (R)econstruction of (C)ancer (K)aryotypes (both clone- and haplotype-specific)
- readcomb — Fast detection of recombinant reads in BAMs
- READemption — A RNA-Seq Analysis Pipeline
- readtagger — Tags reads in a BAM file based on other BAM files.
- reallyrun — Not your grandmas NGS analysis - software for analyzing FASTQs from REALLY libraries
- refgenDetector — refgenDetector
- regSNP — Predict disease-causing probability of human intronic SNVs.
- regsnp-intron — Predict disease-causing probability of human intronic SNVs.
- rev-seqs — Revert sequences to consensus
- reveal — Graph based multi genome aligner
- rfcommands — Set of command line tools used by RiboFlow pipeline.
- RiboCode — A package for identifying the translated ORFs using ribosome-profiling data
- ribogadgets — Hierarchichal data format based on hdf5 for ribosome profiling data
- riboloco — Riboseq analysis
- RiboMetric — A python command-line utility for the generation of comprehensive reports on the quality of ribosome profiling (Ribo-Seq) datasets
- RiboMiner — A python toolset for mining multi-dimensional features of the translatome with ribosome profiling data
- riboplot — Plot read counts of RiboSeq data from BAM format alignment files
- ribopy — Tools for creating and reading Ribo files.
- RiboSeq-DP-Tools — A python command-line utility for working with RiboSeq.Orgs Data Portal
- ribotish — Python Modules for Riboseq data analysis.
- ribotricer — Python package to detect translating ORFs from Ribo-seq data
- riqc — Alignment-free RNA degradation tool
- rlpipes — A standardized R-loop-mapping pipeline
- RNA-APoGee — A package for aligning RNA-seq data without reference biases
- rna-cd — RNA contamination detector
- rnakinet — Package for predicting 5EU in nanopore reads and predicting RNA halflives
- RNFtools — RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
- roprokka — An add on function to consolidate Prokka output
- rough-graph-mapper — Rough Graph Mapper
- RSeQC — RNA-seq QC Package
- RUST — Unit step transformation of Ribo-Seq data
- sam2fasta — Simple script to convert sam file to fasta format.
- sam2lca — Lowest Common Ancestor on SAM/BAM/CRAM alignment files
- samsift — SAMsift - sift your alignments
- samwell — Useful utilities for biological data formats and analyses
- sc-catnip — sc-catnip - single-cell chromatin accessibility analysis tools in python
- sc-tools — sc-tools - Analysis Tools for Single-Cell Data
- sc-utils — sc-utils: utility functions for single-cell analysis.
- ScaleHD — Automated DNA micro-satellite genotyping.