UNMAINTAINED.md

Unmaintained Tools

Tools hosted in repos with no activity in 2+ years.

Data Management

• Send stdout to a Google Sheet: https://github.com/kren1/tosheets
  • Status: Last push 2096 days ago (2020-07-14), 3 open issues

Data Sets

• Large medical datasets for ML: https://github.com/beamandrew/medical-data
  • Status: Last push 873 days ago (2023-11-19), 16 open issues

General Programming Resources

C/C++

• Fast bitwise operations on nucleotide sequences: https://github.com/kloetzl/biotwiddle

  • Status: Last push 2759 days ago (2018-09-21), 0 open issues

• Counting quotient filter: https://github.com/splatlab/cqf

  • Status: Last push 981 days ago (2023-08-03), 3 open issues

• Blazing signature filter: fast pairwise comparison of e.g. gene expression matrices https://github.com/PNNL-Comp-Mass-Spec/bsf-py

  • Status: Last push 3217 days ago (2017-06-19), 0 open issues

Databases

• In-memory key-value db in python: https://github.com/paxos-bankchain/subconscious
  • Status: Last push 2817 days ago (2018-07-25), 1 open issues

Python

• A regular expression scanner: https://github.com/mitsuhiko/python-regex-scanner

  • Status: Last push 3298 days ago (2017-03-31), 2 open issues

• Fast microservices: https://github.com/squeaky-pl/japronto

  • Status: Last push 970 days ago (2023-08-14), 92 open issues

• Template for scientific projects: https://github.com/uwescience/shablona

  • Status: Last push 1069 days ago (2023-05-08), 28 open issues

• Fast and memory-efficient object counting: https://github.com/RaRe-Technologies/bounter

  • Status: Last push 1238 days ago (2022-11-20), 19 open issues

• Working with time-series data: https://github.com/RJT1990/pyflux

  • Status: Last push 899 days ago (2023-10-24), 93 open issues

• Global optimization: https://github.com/chrisstroemel/Simple

  • Status: Last push 2994 days ago (2018-01-29), 6 open issues

• HPAT: framework for automatically parallizing numpy and pandas code using MPI https://github.com/IntelLabs/hpat

  • Status: Archived repo

• B+ Tree: Hash table backed by on-disk storage https://github.com/NicolasLM/bplustree

  • Status: Last push 2580 days ago (2019-03-18), 5 open issues

• Launch an editor from python: https://github.com/fmoo/python-editor

  • Status: Last push 913 days ago (2023-10-11), 13 open issues

R

Data Cleaning

• daff: diff/merge for data frames - https://github.com/edwindj/daff

  • Status: Last push 786 days ago (2024-02-15), 13 open issues

• magrittr/pipes

  • debugging: https://github.com/gaborcsardi/tamper
  • Status: Archived repo

Misc

• Access to Google spreadsheets from R: https://github.com/jennybc/googlesheets

  • Status: Archived repo

• Developing R packages: https://github.com/jtleek/rpackages

  • Status: Last push 821 days ago (2024-01-10), 4 open issues

• Make for R: https://github.com/richfitz/maker

  • Status: Last push 4082 days ago (2015-02-06), 0 open issues

Reproducibility/Containerization

• Continuous analysis: https://github.com/greenelab/continuous_analysis
  • Status: Last push 1947 days ago (2020-12-10), 1 open issues

Building Pipelines

• Qsubsec: template language for defining SGE workflows https://github.com/alastair-droop/qsubsec

  • Status: Last push 1136 days ago (2023-03-01), 1 open issues

• Reflow: workflow management system developed by Grail https://github.com/grailbio/reflow

  • Status: Last push 905 days ago (2023-10-18), 28 open issues

• https://github.com/calebwin/pipelines

  • Status: Last push 2366 days ago (2019-10-18), 2 open issues

Software Distribution

• Executable archives (xar): https://github.com/facebookincubator/xar

  • Status: Archived repo

• Parameter optimization

  • Spearmint: https://github.com/beamandrew/Spearmint
  • Status: Last push 3118 days ago (2017-09-26), 0 open issues

• Debugging

  • Sandsifter: Fuzzer https://github.com/xoreaxeaxeax/sandsifter
  • LivePython: https://github.com/agermanidis/livepython
  • Status: Last push 780 days ago (2024-02-20), 64 open issues

Genomics

Algorithms

• Fast BWT creation: https://github.com/hitbc/deBWT
  • Status: Last push 3687 days ago (2016-03-07), 0 open issues

Assay Design

• Choosing assays based on complementarity to existing data: https://github.com/melodi-lab/Submodular-Selection-of-Assays
  • Status: Last push 3475 days ago (2016-10-04), 0 open issues

Candidate Prioritization

• Bayesian prioritizaiton of rare functional variants using RNA-seq data: https://github.com/ipw012/RIVER
  • Status: Last push 2227 days ago (2020-03-05), 2 open issues

Data Formats

• Fast ordered sampling of records: https://github.com/tonymugen/sampleSNPs/

  • Status: Last push 1914 days ago (2021-01-12), 0 open issues

• Generate NCBI submission data: https://github.com/genomeannotation/GAG

  • Status: Last push 2958 days ago (2018-03-05), 14 open issues

• Generic format for storing alignment incidence data https://github.com/churchill-lab/alntools

  • Status: Last push 1085 days ago (2023-04-22), 8 open issues

General Information

• Mappings between contig names in different assemblies: https://github.com/dpryan79/ChromosomeMappings
  • Status: Last push 1230 days ago (2022-11-28), 1 open issues

Microarray

• Imputation QC: https://github.com/inzilico/imputeqc
  • Status: Last push 2083 days ago (2020-07-27), 2 open issues

Motif/TFBS

• Cell type-specific TFBS analysis (focuses analysis on TFs expressed in cell type of interest): https://github.com/Danko-Lab/rtfbs_db

  • Status: Last push 2676 days ago (2018-12-12), 0 open issues

• Bayesian motif discovery: https://github.com/soedinglab/BaMMmotif

  • Status: Last push 3109 days ago (2017-10-05), 0 open issues

• CRBM: https://github.com/schulter/crbm

  • Status: Last push 3064 days ago (2017-11-20), 0 open issues

• YAMDA: https://github.com/daquang/YAMDA

  • Status: Last push 2648 days ago (2019-01-10), 4 open issues

• Clustering of peaks: https://github.com/BackofenLab/StoatyDive

  • Status: Last push 1390 days ago (2022-06-21), 1 open issues

Network Analysis

• Similarity search: https://github.com/zhangjiaobxy/nssrfPackage
  • Status: Last push 3152 days ago (2017-08-24), 0 open issues

Population genetics

• Population history from unphased whole-genomes: https://github.com/popgenmethods/smcpp

  • Status: Last push 811 days ago (2024-01-20), 103 open issues

• Calculation of LD from genome-wide genotype likelihoods: https://github.com/fgvieira/ngsLD

  • Status: Last push 879 days ago (2023-11-13), 2 open issues

Prediction

• eQTL

  • Imputation of gene expression from genotype data : https://github.com/hriordan/PrediXcan
  • Status: Last push 1272 days ago (2022-10-17), 6 open issues

• Methylation

  • CpGenie: predicts methylation from sequence, predicts impact of variants on nearby methylation https://github.com/gifford-lab/CpGenie
  • Status: Last push 2703 days ago (2018-11-15), 2 open issues

• Classification of cis-regulatory modules: https://github.com/weiyangedward/IMMBoost

  • Status: Last push 3520 days ago (2016-08-20), 0 open issues

• Imputation: https://github.com/tdurham86/PREDICTD

  • Status: Last push 2976 days ago (2018-02-16), 0 open issues

• Variable selection for random forest: https://github.com/jomayer/SMuRF

  • Status: Last push 3238 days ago (2017-05-29), 1 open issues

Sequence Analysis

Chromatin Interactions

• Predict enhancer targets: https://github.com/shwhalen/targetfinder

  • Status: Last push 1892 days ago (2021-02-03), 0 open issues

• Call CNVs and translocations https://github.com/parklab/HiNT

  • Status: Last push 1710 days ago (2021-08-04), 22 open issues

DNA

• Read Clustering

  • PE UMI-tagged reads: https://github.com/vpc-ccg/calib
  • Status: Last push 1039 days ago (2023-06-06), 3 open issues

• Repeat calling

  • REPdenovo: https://github.com/Reedwarbler/REPdenovo
  • Status: Last push 1778 days ago (2021-05-29), 8 open issues

• Polygenic scores

  • https://github.com/brentp/nimpress
  • Status: Last push 2380 days ago (2019-10-04), 0 open issues

• Amplicon

  • Pisces: https://github.com/Illumina/Pisces/
  • Status: Last push 1388 days ago (2022-06-22), 57 open issues

Footprinting

• https://github.com/Boyle-Lab/TRACE
  • Status: Last push 1044 days ago (2023-06-01), 6 open issues

General-purpose

• chopBAI: segment BAM indexes by region for faster access https://github.com/DecodeGenetics/chopBAI

  • Status: Last push 3663 days ago (2016-03-30), 2 open issues

• multi-mapping reads

  • MMR: https://github.com/ratschlab/mmr
  • SmartMap: https://github.com/shah-rohan/SmartMap
  • Status: Last push 3341 days ago (2017-02-15), 3 open issues

• Normalization:

  • GLScale: https://github.com/allenxhcao/glscale
  • QSmooth: https://github.com/stephaniehicks/qsmooth
  • ORNA: https://github.com/SchulzLab/ORNA
  • Suquan: https://github.com/jpvert/suquan
  • Status: Last push 3602 days ago (2016-05-31), 2 open issues

• Detection and removement of barcode swapping (issue on Illumina sequencers that used patterned flow cells: https://github.com/MarioniLab/BarcodeSwapping2017

  • Status: Last push 2837 days ago (2018-07-05), 0 open issues

• Data processing pipelines for many types of omics data, built using NextFlow and Singularity: https://github.com/c-guzman/cipher-workflow-platform

  • Status: Last push 3031 days ago (2017-12-22), 3 open issues

• Recover unaligned reads: https://github.com/VCCRI/Scavenger

  • Status: Last push 2213 days ago (2020-03-19), 0 open issues

• Mantis: index of raw-read datasets for efficient and exacty queries https://github.com/splatlab/mantis

  • Status: Last push 764 days ago (2024-03-07), 8 open issues

• Machine learning method for determining sequence identity: https://github.com/TulsaBioinformaticsToolsmith/FASTCAR

  • Status: Last push 2523 days ago (2019-05-14), 1 open issues

• Progressive MSA (DNA or protein) with indel evolution: https://github.com/acg-team/ProPIP

  • Status: Last push 1711 days ago (2021-08-04), 3 open issues

• Query compressed GFF/GTF files https://github.com/qm2/gpress

  • Status: Last push 919 days ago (2023-10-05), 0 open issues

• Create consensus genomes https://github.com/kaminow/consdb

  • Status: Last push 1158 days ago (2023-02-07), 2 open issues

• Score arbitrary regions by sequence difference from a reference population https://github.com/machine2learn/QGS

  • Status: Last push 946 days ago (2023-09-07), 0 open issues

• Adapter Trimming

  • Discover adapter sequences: https://github.com/chc-code/FindAdapt
  • Status: Last push 827 days ago (2024-01-04), 2 open issues

MNase-seq

• Alternative/differential nuleosome positioning: https://github.com/airoldilab/cplate
  • Status: Last push 3515 days ago (2016-08-26), 0 open issues

Metagenomics

• Alignment-free functional binning and abundance estimation: https://github.com/snz20/carnelian

  • Status: Last push 1893 days ago (2021-02-02), 1 open issues

• Taxonomic classificatino using pseudoalignment: https://github.com/mreppell/Karp

  • Status: Last push 3128 days ago (2017-09-16), 4 open issues

Methylation

• SNP calling

  • BS-SNPer: fast SNP calling from bisulfite-converted sequencing reads https://github.com/hellbelly/BS-Snper
  • https://github.com/bio15anu/revelio
  • Status: Last push 1822 days ago (2021-04-15), 16 open issues

• Haplotype calling

  • https://github.com/ZhouQiangwei/MethHaplo
  • Status: Last push 906 days ago (2023-10-18), 11 open issues

• Microarray

  • Call CNVs from methylation array data: https://github.com/mknoll/cnAnalysis450k
  • Status: Last push 3195 days ago (2017-07-12), 0 open issues

Nanopore/PacBio

• Signal-level barcode demux: https://github.com/rrwick/Deepbinner

  • Status: Last push 1908 days ago (2021-01-18), 32 open issues

• Real-time base calling with read-until: https://github.com/harrisonedwards/RUBRIC

  • Status: Archived repo

• https://github.com/nanoporetech/wub

  • Status: Archived repo

• Detect analytes from raw event data: https://github.com/nanoporetech/mako

  • Status: Last push 2819 days ago (2018-07-23), 0 open issues

Peak-based

ChIP-seq

• Chilin: https://github.com/cfce/chilin

  • Status: Last push 1848 days ago (2021-03-19), 3 open issues

• EM algorithm for cooperatively bound TFs: https://github.com/vishakad/cpi-em

  • Status: Last push 3308 days ago (2017-03-20), 0 open issues

• Pipelines

  • ChIPSeqFPro: https://github.com/milospjanic/ChIPSeqFPro
  • Status: Last push 3222 days ago (2017-06-15), 0 open issues

• Shape motifs: https://github.com/h-samee/shape-motif

  • Status: Last push 2638 days ago (2019-01-19), 3 open issues

• Branch of MACS for improved weighting of controls: https://github.com/aawdeh/MACS/tree/WACS

  • Status: Last push 2422 days ago (2019-08-24), 0 open issues

• MAnorm2 https://github.com/tushiqi/MAnorm2

  • Status: Last push 1255 days ago (2022-11-03), 6 open issues

• Motif discovery:

  • K-mer based without peak calling https://github.com/menzel/nopeak
  • Status: Last push 1067 days ago (2023-05-09), 2 open issues

Chromatin accessibility

• DNase footprinting: https://github.com/ajank/Romulus

  • Status: Last push 2592 days ago (2019-03-06), 0 open issues

• Predict TF binding affinities using open chromatin + PWMs: https://github.com/schulzlab/TEPIC

  • Status: Last push 1446 days ago (2022-04-26), 4 open issues

• Nucleotide-specific bias adjustment: https://github.com/txje/sequence-bias-adjustment

  • Status: Last push 2122 days ago (2020-06-18), 0 open issues

• Deep learning-based denoiser https://github.com/clara-parabricks/AtacWorks

  • Status: Last push 1149 days ago (2023-02-16), 26 open issues

• Simulation

  • https://github.com/bowang-lab/simATAC
  • Status: Last push 1903 days ago (2021-01-23), 2 open issues

QC

• Batch effects:

  • BatchQC: https://github.com/mani2012/BatchQC
  • Correct batch effects using residual neural net: https://github.com/ushaham/BatchEffectRemoval
  • Status: Last push 960 days ago (2023-08-25), 11 open issues

• ChronQC: https://github.com/nilesh-tawari/ChronQC

  • Status: Last push 2482 days ago (2019-06-25), 3 open issues

• Historical tracking: https://github.com/nilesh-tawari/ChronQC

  • Status: Last push 2482 days ago (2019-06-25), 3 open issues

• Protocol-specific pre-processing: https://github.com/lh3/pre-pe

  • Status: Last push 2843 days ago (2018-06-28), 2 open issues

• https://github.com/DecodeGenetics/read_haps

  • Status: Last push 2038 days ago (2020-09-10), 0 open issues

• RabbitQC

  • Status: Last push 1391 days ago (2022-06-20), 3 open issues

• determine organism, assay type, and sequencing platform from k-mer frequencies https://github.com/DaehwanKimLab/seqwho

  • Status: Last push 1541 days ago (2022-01-21), 1 open issues

• https://github.com/reneshbedre/HTSeqQC

  • Status: Last push 1725 days ago (2021-07-21), 0 open issues

• https://github.com/Griffan/FASTQuick

  • Status: Last push 1882 days ago (2021-02-14), 1 open issues

• https://github.com/DaehwanKimLab/seqwho

  • Status: Last push 1541 days ago (2022-01-21), 1 open issues

RNA

• Differential transcript usage
  • Rats: https://github.com/bartongroup/Rats
  • Bayesian extenstion to BitSeq for differential transcript usage: https://github.com/mqbssppe/cjBitSeq
  • From Kallisto/Salmon ECCs: https://github.com/Oshlack/ec-dtu-paper
  • Status: Last push 1408 days ago (2022-06-03), 2 open issues

Single-cell

• Allele-specific expression

  • SCALE accounts for "burstiness" of transcription: https://github.com/yuchaojiang/SCALE
  • scBASE: https://github.com/churchill-lab/scBASE
  • https://github.com/anna-saukkonen/PAC
  • Status: Last push 2003 days ago (2020-10-15), 3 open issues

• Methylation

  • Prediction of missing information: https://github.com/cangermueller/deepcpg
  • Mapping: https://github.com/wupengomics/scBS-map
  • Status: Last push 2385 days ago (2019-09-30), 17 open issues

• HLA

  • https://github.com/10XGenomics/scHLAcount
  • Status: Last push 1617 days ago (2021-11-05), 15 open issues

Somatic

• Personal reference editor: https://github.com/precisionomics/PRESM

  • Status: Last push 2496 days ago (2019-06-10), 0 open issues

• Correct FFPE artifacts

  • https://github.com/QingliGuo/FFPEsig
  • https://github.com/mmaitenat/ideafix
  • Status: Last push 814 days ago (2024-01-17), 0 open issues

• MMR

  • https://github.com/xqzou/MMRDetect
  • Status: Last push 1827 days ago (2021-04-09), 0 open issues

Simulation

• GWAS: https://github.com/chr1swallace/simGWAS
  • Status: Last push 1783 days ago (2021-05-24), 0 open issues

Variant annotation

• Normalization of SNP ID's from literature: https://github.com/rockt/SETH

  • Status: Last push 780 days ago (2024-02-21), 17 open issues

• Tissue-specific https://github.com/kevinVervier/TiSAn

  • Status: Last push 2699 days ago (2018-11-19), 0 open issues

• Constrained coding regions: https://github.com/quinlan-lab/ccrhtml

  • Status: Last push 2363 days ago (2019-10-22), 0 open issues

• Clinical annotation: https://github.com/ding-lab/CharGer

  • Status: Last push 1487 days ago (2022-03-15), 10 open issues

• Individual, per-gene pathogenicity scores: https://github.com/UoS-HGIG/GenePy

  • Status: Last push 1675 days ago (2021-09-08), 2 open issues

• https://github.com/mulinlab/VarNote

  • Status: Last push 1441 days ago (2022-05-01), 6 open issues

• Allele Dispersion Score: how population-specific is a variant? https://github.com/wassermanlab/ADS

  • Status: Last push 1520 days ago (2022-02-10), 0 open issues

Pairwise alignment

Algorithms

General

• GASAL2: GPU-accelerated alignment https://github.com/nahmedraja/GASAL2

  • Status: Last push 1354 days ago (2022-07-27), 11 open issues

• Stdaln: Fast dynamic programming algorithm by Heng Li: https://github.com/jts/nanopolish/tree/master/src/thirdparty

  • Status: Last push 979 days ago (2023-08-05), 94 open issues

• There is the possibility to apply techniques from short-read aligners to pairwise alignment, e.g. seed-and-chain. Some useful algorithms are available in Modular Aligner: https://github.com/ITBE-Lab/MA

  • Status: Last push 998 days ago (2023-07-18), 4 open issues

• https://github.com/CMU-SAFARI/Scrooge

  • Status: Last push 1023 days ago (2023-06-23), 2 open issues

Global

• NW implementations with affine and linear gap penalties: https://github.com/AYahi/recNW

  • Status: Last push 2824 days ago (2018-07-17), 1 open issues

• Parameter-free, context-specific scoring (optimized for long repeats): https://github.com/seryrzu/unialigner

  • Status: Last push 732 days ago (2024-04-09), 9 open issues

• https://github.com/ruanjue/bsalign

  • Status: Last push 1068 days ago (2023-05-09), 3 open issues

Local

• GPU-accelerated Smith-Waterman for nucleotides or proteins: https://github.com/mgawan/GPU-BSW
  • Status: Last push 1657 days ago (2021-09-26), 3 open issues

Semi-global

• Skewer algorithm: bit-masked k-difference matching (in C++): https://github.com/relipmoc/skewer

  • Status: Last push 1297 days ago (2022-09-21), 41 open issues

• Adaptive banded alignment:

  • https://github.com/ocxtal/libgaba
  • https://github.com/ocxtal/adaptivebandbench
  • Status: Last push 2898 days ago (2018-05-04), 4 open issues

• Nepal: https://github.com/yamada-kd/nepal

  • Status: Last push 2986 days ago (2018-02-06), 0 open issues

• BGSA: provides accelerated implementation of the BitPAl algorithm https://github.com/sdu-hpcl/BGSA

  • Status: Last push 1504 days ago (2022-02-27), 3 open issues

Other

• Test whether different sequence encodings might enable faster alignment https://github.com/hammerlab/kerseq/blob/master/kerseq/sequence_encoding.py
  • Status: Last push 3810 days ago (2015-11-05), 0 open issues

Proteomics

MSA

• https://github.com/clairemcwhite/vcmsa
  • Status: Last push 904 days ago (2023-10-20), 6 open issues

Publication/Archiving

Code/Data sharing

• Git plugin for version-control of data files: https://github.com/ctjacobs/git-rdm
  • Status: Last push 3091 days ago (2017-10-24), 0 open issues

Posters

• Using RMarkdown: https://github.com/brentthorne/posterdown

  • Status: Last push 1578 days ago (2021-12-15), 39 open issues

• "Better Poster" template in R-markdown: https://github.com/brentthorne/posterdown

  • Status: Last push 1578 days ago (2021-12-15), 39 open issues

Slides

• Using Markdown: https://github.com/arnehilmann/markdeck
  • Status: Last push 1162 days ago (2023-02-04), 10 open issues

Writing

• Convert between (R)markdown and iPython notebooks: https://github.com/aaren/notedown

  • Status: Last push 1635 days ago (2021-10-18), 47 open issues

• Continuous analysis: https://github.com/greenelab/continuous_analysis

  • Status: Last push 1947 days ago (2020-12-10), 1 open issues

• Desktop app for searching/managing papers: https://github.com/codeforscience/sciencefair

  • Status: Last push 2104 days ago (2020-07-07), 47 open issues

Statistics/Machine Learning

Methods/algorithms

• Identification of correlated features within or between datasets: https://github.com/siskac/discordant

  • Status: Last push 1527 days ago (2022-02-03), 6 open issues

• Bayesian alternatives to standard R functions: https://github.com/rasmusab/bayesian_first_aid

  • Status: Last push 3537 days ago (2016-08-03), 7 open issues

• Analysis of mutual information: https://github.com/jkleinj/arMI

  • Status: Last push 2818 days ago (2018-07-24), 0 open issues

• Iterative denoising tree: https://github.com/youngser/behaviotypes/blob/master/doidt.r

  • Status: Last push 2724 days ago (2018-10-26), 2 open issues

• Visualizing ML features: https://github.com/pair-code/facets

  • Status: Archived repo

• Iterative random forest: https://github.com/sumbose/iRF

  • Status: Last push 1866 days ago (2021-03-02), 4 open issues

• Polynomial regression: https://github.com/matloff/polyreg

  • Status: Last push 1407 days ago (2022-06-03), 12 open issues

• Alternative importance score for random forrest classifiers: https://github.com/StephanSeifert/SurrogateMinimalDepth

  • Status: Archived repo

• Feature generation from sequences: https://github.com/mrzResearchArena/PyFeat/

  • Status: Last push 1336 days ago (2022-08-14), 1 open issues

Python

• Linear mixed-model solver https://github.com/nickFurlotte/pylmm

  • Status: Last push 3771 days ago (2015-12-14), 2 open issues

• Exact inference in HMMs with large number of hidden states: https://github.com/regevs/factorial_hmm

  • Status: Last push 2138 days ago (2020-06-03), 1 open issues

• Library for preprocessing various NGS formats for input into Keras or other DL libraries: https://github.com/BIMSBbioinfo/janggu

  • Status: Last push 1655 days ago (2021-09-29), 3 open issues

Text classification

• fastText: https://github.com/facebookresearch/fastText

  • Status: Archived repo

• Second-generation p-values: https://github.com/lucymcgowan/sgpvalue

  • Status: Last push 2768 days ago (2018-09-11), 0 open issues

• Convert sequence alignments into features for machine learning: https://github.com/ekg/hhga

  • Status: Last push 2493 days ago (2019-06-13), 12 open issues

Visualization

Javascript

• Genome browser components: https://github.com/Zhong-Lab-UCSD/Genomic-Interactive-Visualization-Engine
  • Status: Last push 1192 days ago (2023-01-05), 29 open issues

Networks

• Human-like Orthogonal Layout: https://github.com/skieffer/hola
  • Status: Last push 2618 days ago (2019-02-08), 0 open issues

Phylogenetic trees

• scripts from Holt lab: https://github.com/katholt/plotTree

  • Status: Last push 3564 days ago (2016-07-08), 14 open issues

• TreeLink: https://github.com/allendecid/TreeLink

  • Status: Last push 3747 days ago (2016-01-06), 0 open issues

Python

• Vincent: https://github.com/wrobstory/vincent

  • Status: Archived repo

• https://github.com/svaksha/pythonidae/blob/master/Computer-Graphics.md

  • Status: Last push 1011 days ago (2023-07-04), 3 open issues

• 2D visualization of DNA sequences: https://github.com/Lab41/squiggle

  • Status: Archived repo

R

• Nice looking boxplots: https://github.com/mw55309/perceptions

  • Status: Last push 3270 days ago (2017-04-28), 0 open issues

• kmerPyramid: https://github.com/jkruppa/kmerPyramid

  • Status: Last push 3221 days ago (2017-06-16), 0 open issues

• shinyCircos: https://github.com/venyao/shinyCircos

  • Status: Last push 1293 days ago (2022-09-25), 5 open issues

• Create pallete from colors in an image: https://github.com/AndreaCirilloAC/paletter

  • Status: Last push 1199 days ago (2022-12-29), 0 open issues

Data Types

• Shushi: publication-quality figures from multiple data types https://github.com/dphansti/Sushi

  • Status: Last push 1627 days ago (2021-10-26), 13 open issues

• Interaction data: https://github.com/kcakdemir/HiCPlotter

  • Status: Last push 2097 days ago (2020-07-13), 0 open issues

ggplot2

• superheat: pretty heatmaps https://github.com/rlbarter/superheat

  • Status: Last push 2041 days ago (2020-09-07), 27 open issues

• joyplots: https://github.com/clauswilke/ggjoy

  • Status: Last push 2885 days ago (2018-05-18), 0 open issues

• colorbindr: test effect of colorblindness on readability of plots https://github.com/clauswilke/colorblindr

  • Status: Last push 998 days ago (2023-07-17), 9 open issues

• Theme using IBM Plex fonts: https://github.com/juliasilge/silgelib/blob/master/R/graphing.R

  • Status: Last push 1269 days ago (2022-10-19), 0 open issues

• Visualization of feature density along the genome: https://github.com/sguizard/DensityMap

  • Status: Last push 1430 days ago (2022-05-12), 2 open issues

• libvips: fast imgae processing library (C++ and python bindings) https://github.com/jcupitt/libvips

  • Status: Last push 1662 days ago (2021-09-22), 0 open issues

• Interactive reports: https://github.com/Genomon-Project/paplot

  • Make plots from regions of BAM files
  • Useful for very deep sequencing
  • Status: Last push 1165 days ago (2023-02-01), 1 open issues