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Projects in Awesome Lists by alexpreynolds
A curated list of projects in awesome lists by alexpreynolds .
https://github.com/alexpreynolds/sample
Performs memory-efficient reservoir sampling on very large input files delimited by newlines
bed bioinformatics c genomics reservoir-sampling sampling
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-counter
Count kmers with a more efficient (faster) hash table
bioinformatics cpp14 genomics hash-map kmer kmer-counting
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/soda
Python-based UCSC genome browser snapshot-taker and gallery-maker
bed genomics python ucsc visualization
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/biostar-handbook-web
Online companion for the Biostar Handbook.
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-collapse
Collapse a set of redundant kmers to use IUPAC degenerate bases
bioinformatics encoding iupac kmer
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/tabix-service
A nodejs-based service for requests for tabix-indexed genomic data
bioinformatics genomics genomics-visualization nodejs samtools tabix web-service
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/hglive
HiGlass-backed dynamic BED gallery browser
bed bioinformatics expressjs higlass javascript react visualization
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/higlass-tabix-datafetcher
Provide remote access to remotely-hosted tabix files to HiGlass client applications
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/convert2bed
Convert common binary and text genomic formats to BED
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/byte-store
Generate and explore upper triangular and square matrices of 1-byte values
bioinformatics c correlation-scores encoding jaccard-similarity pearson spearman-rho
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/react-seqlogo
React sequence logo component
bioinformatics d3 information-theory react react-components reactjs sequence-logo
Last synced: 27 Oct 2024
https://github.com/alexpreynolds/filter-regions
Filter genomic regions by score and proximity
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/disjoint-windows
Build a list of high-scoring, non-overlapping intervals using sampling or scheduling methods
bedops bioinformatics disjoint genome packing priority-queue sample scheduling-algorithms
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/hilbert-genome-cooler
Exploring the Cooler format to store whole-genome datasets arranged into a Hilbert curve
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/decode_m6a_events
Decode m6A events and probabilities from BAM MM/ML tag data
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/subset
Draw a subset of lines from a text file
cplusplus-14 genomics sample sampling subset text-processing
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/threejs-text-test
Test rendering a canvas text element to the threejs DOM
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/nearest-transcripts
Return nearest per-gene transcripts within N bases of some set of regions
bioinformatics set set-operations
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/ideogram-viewer-react-test
React-based test of the eweitz ideogram plugin
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/freq-counter
Count letter frequencies in sliding windows over a genome
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/starch-efficiency
Test the relative efficiency of starch --bzip2 and --gzip options on random BED data
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/simd-pearson-test
Test use of SIMD/SSE to calculate Pearson r correlation
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/region-selection
Methods for filtering for high-scoring genomic intervals
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/starch3
Multi-threaded genomic data compression
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/react-cube
React 3d scatterplot component with WebGL support
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/rts
Random triangular matrix sampler
cplusplus-14 matrix matrix-calculations matrix-sampling sample sampling
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-counter-sparse
Count canonical kmers with Google sparse_hash_map
bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-counter-ska
Count canonical kmers with Malte Skarupke's bytell_hash_map hash table
bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-counter-unordmap
Count canonical kmers with STL unordered_map
bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/matrix2svg
Converts a text-formatted matrix to a vector-based SVG figure
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-counter-boost
Count canonical kmers with Boost C++ `boost::unordered_map` hash table
bazel bazel-examples bioinformatics boost cpp hash-tables kmer kmer-counting kmer-frequency-count
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-boolean
Test if a kmer is or is not in a set of sequences
bioinformatics cpp14 kmer kmer-composition python
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/eforge-www
Web client and services for eFORGE
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/generic-list-react-app
Read in a list of strings from a file and render it to a pull-down in React
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/colormaker
Starting with a seed color and desired number of colors, returns an array of colors
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-counter-abseil
Count canonical kmers with Abseil C++ `absl::flat_hash_map`
abseil bazel bazel-examples bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/kmer-counter-emilib
Count canonical kmers with Emil Ernerfeldt's emilib::HashMap
bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/hilbert-genome
Using space-fitting curves to visualize and explore the genome
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/indel-relative-frequency-viewer
Indel viewer
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/flow-cytometry-visualization
Flow cytometry visualization demo using Jupyter, Plotly, and fcsparser
bioinformatics fcs jupyter jupyter-notebook plotly puppeteer python3 visualization
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/annotation-lookup-service
Web service for adding and querying a genomic annotation set for an entry identifier
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/dhs-bed12-to-bam
Convert Index DHS BED12 representation to BAM
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/automata
Automata is a small library for generating one-dimensional, two-color cellular automata
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/cull-exemplars
Filter lower-scoring, neighboring genomic intervals within a specified distance
bed bedops bioinformatics interval set set-operations
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/annotations
Expressjs + Redis-backed annotations web service with autocomplete
bioinformatics expressjs nodejs redis redis-server service
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/fire-bed11-to-sam
Convert FIRE-linker-nucleosome data in BED11 to SAM
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/zlib-test
Tests the per-line extraction of a zlib stream
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/svg-animation-test
A project to test SVG element animation
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/svg-animation-tapestry-test-v2
A project to test animation of a tapestry of copied SVG elements
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/higlass-bigbed-datafetcher
Provide remote access to remotely-hosted bigBed files to HiGlass client applications
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/tfbs-bed7-to-sam
Convert TFBS data in BED6+1 to SAM
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/react-higlass-test
Test bench for HiGlass-based React application
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/targetscope
Client-side targetscope project resources
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/react-scrollwheel-test
Testing scrollwheel events in a React environment
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/barebones-higlass
A barebones test of higlass and modified plugs outside of the usual web app context
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/svg-animation-tapestry-test
A project to test animation of a tapestry of copied SVG elements
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/svg-animation-tapestry-test-v3
A project to test animation of a tapestry of copied SVG elements
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/react-seqlogo-demo
Sequence logo generation with d3
bioinformatics d3 react react-components sequence-logo
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/recommender-proxy
Web service to pattern matching and retrieval tool
Last synced: 07 Nov 2024
https://github.com/alexpreynolds/higlass-pileup-test
Testing development and production build capability of higlass and higlass-pileup
Last synced: 07 Nov 2024