Hoohm's Stars
W4RH4WK/Debloat-Windows-10
A Collection of Scripts Which Disable / Remove Windows 10 Features and Apps
python-jsonschema/jsonschema
An implementation of the JSON Schema specification for Python
ossu/math
🧮 Path to a free self-taught education in Mathematics!
NAalytics/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273
RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.
BingLingGroup/autosub
Command-line utility to transcribe/translate from video/audio/subtitles to subtitles
mhamilton723/FeatUp
Official code for "FeatUp: A Model-Agnostic Frameworkfor Features at Any Resolution" ICLR 2024
kblin/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
Primer-Learning/PrimerToolsUnity
Tool used for producing Primer YouTube videos
christophergandrud/networkD3
D3 JavaScript Network Graphs from R
xhluca/dl-translate
Library for translating between 200 languages. Built on 🤗 transformers.
tournesol-app/tournesol
Free and open source code of the https://tournesol.app platform. Meet the community on Discord https://discord.gg/WvcSG55Bf3
NVIDIA-Genomics-Research/rapids-single-cell-examples
Examples of single-cell genomic analysis accelerated with RAPIDS
althonos/pronto
A Python frontend to (Open Biomedical) Ontologies.
daattali/shinyforms
📝 Easily create questionnaire-type forms with Shiny
AdeelK93/collapsibleTree
Create Interactive Collapsible Tree Diagrams in R using D3.js
plger/scDblFinder
Methods for detecting doublets in single-cell sequencing data
parashardhapola/scarf
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
jmbreda/Sanity
Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
bitsofwinter/cryptotaxsweden
Script for generating a tax report for cryptocurrency trading which can be sent to the Swedish tax authorities.
LuciAkirami/liva
LIVA - Local Intelligent Voice Assistant
faryabib/too-many-cells
Cluster single cells and analyze cell clade relationships with colorful visualizations.
rajewsky-lab/spacemake
chaichontat/samui
A performant scientific image visualization system.
numbersprotocol/capture-lite
A photo-sharing app with only verifiable photos and videos.
sararselitsky/FastPG
Fast phenograph, CyTOF
ion-elgreco/polars-distance
Polars plugin for pairwise distance functions
CircuitLord/NotReaper
A mapper for the VR rhythm game Audica
tk382/HIPPO
Heterogeneity Induced Pre-Processing tOol
iamsnn/autosub
Command-line utility to transcribe/translate from video/audio/subtitles to subtitles
brentscott93/shinyforms
Easily create questionnaire-type forms with Shiny