Package: NestLink 1.28.0

Lennart Opitz

NestLink: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles

Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich.

Authors:Pascal Egloff [aut], Iwan Zimmermann [ctb], Fabian M. Arnold [ctb], Cedric A.J. Hutter [ctb], Lennart Opitz [aut, cre], Lucy Poveda [ctb], Hans-Anton Keserue [ctb], Christian Panse [aut, ctb], Bernd Roschitzki [aut], Markus Seeger [aut]

NestLink_1.28.0.tar.gz
NestLink_1.28.0.tar.gz(r-4.7-any)NestLink_1.28.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NestLink/json (API)

# Install 'NestLink' in R:
install.packages('NestLink', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:NestLink-1.29.0(data/experiment 3.24)NestLink-1.28.0(data/experiment 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

experimenthubexperimentdatasequencingdatamassspectrometrydatareproducibleresearchdatapkg

4.92 score 14 scripts 14 exports 96 dependencies

Last updated from:7102e675cb (on RELEASE_3_23). Checks:1 WARNING, 2 NOTE, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING203
linux-develNOTE544
source / vignettesOK420
linux-releaseNOTE553

Exports:.ssrc.mascotcompose_GPGx8cTermcompose_GPx10Rcompose_GSx7cTermgetExperimentHubFilenamegetFCgetNBnanobodyFlycodeLinking.as.fastananobodyFlycodeLinking.summaryNB.unambiguousNB.uniqueplot_in_silico_LCMS_maprunNGSAnalysistwoPatternReadFilter

Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobcachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdplyrExperimentHubfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegplotsgtoolshttrhttr2hwriterinterpIRangesjpegjsonliteKEGGRESTKernSmoothlambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprotVizpurrrpwalignR6rappdirsRColorBrewerRcppRcppEigenRhtslibrlangRsamtoolsRSQLiteS4ArraysS4VectorsSeqinfoShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml

make-data 4 ExperimentHub
Timeline Plots | Make Data (replaces make-data.R) | NL42_100K.fastq.gz | knownNB.txt | nanobodyFlycodeLinkage.RData | NB.tryptic and FC.tryptic | F255744.RData and WU160118.RData | Mass spec data | Compute the peptide spectrum matches | Workflow available through B-Fabric | make-data for NestLink | PGexport2_normalizedAgainstSBstandards_Peptides.csv | Uploading to S3 | Overview/Getting started using Bioconductor r Biocpkg("ExperimentHub") | Session info | References
Rendered frommake-data.Rmdusingknitr::rmarkdown

Last update: 2019-05-02
Started: 2018-12-18

Link high quality flycodes and nanobody sequences by NGS filtering
Load Package | Load Data | Define Input & Output-Folder | Load known nanobodies (NB) for QC Checks | Set Example Parameters | Run NGS Workflow | Create Input FASTA File for Proteomics Analysis | Session info
Rendered fromlink-nanobodies-flycodes.Rmdusingknitr::rmarkdown

Last update: 2019-02-04
Started: 2019-01-24

FASTA p1875 db10 / WU160118 / R444589 - Postprocessing / Summary
Load requiered R packages | Display ESP | Charge State Frequency | Load workunit 160118 | FlyCode Mass Distribution | Mascot Ion Score Distribution | Compare Real and in-silico FlyCodes | AA design frequency | SSRC Prediction vs. Measured Retention Time | SSRC and Retention Time Distribution | Mass vs. RT Panels - Mascot Ion Score cut-off | Session info | References
Rendered fromanalyze-flycode-detectibilty.Rmdusingknitr::rmarkdown

Last update: 2019-02-04
Started: 2019-01-24

Control experiment to assess robustness of protein detection via flycodes
Getting started | Load data | Clean | Sanity check | Camera ready summary table | Define FCfill2max | Plot compute CVs for each row | Absolute Quantification | Define function FlycodeAbsoluteStatistics using coli1 column | Camera ready absolute table | Define FCrandom | Conduct the random experiment | Camera ready plot of absolute flycode simulation | Relative Quantification | Normalization | Define ratios | Determine outliers (removal) | Detect outlier | Define function FlycodeRelativeStatistics | Camera ready relative table | Session info | References
Rendered fromsupplement-note1.Rmdusingknitr::rmarkdown

Last update: 2019-02-04
Started: 2019-01-24

Derive Peptide Flycodes by Conducting Random Experiment
Input Pool Frequency | Sanity Check | Compose Peptides | GPGXXXXXXXX(VR|VSR|VFGIR|VSGER) peptide | GPYYXXXXXXYYR peptide | Generate peptides | Peptide mass | Compute peptide mass | Draw parent ion mass histogram | Hydrophobicity | Compute Hydrophobicity value using SSRC | Draw hydrophobicity histogram | Quality Control (QC) | QC of composed peptides | Input | Output | Count GP patterns | Compute AA frequency table | Session info | References
Rendered fromsimulate-flycodes.Rmdusingknitr::rmarkdown

Last update: 2019-01-24
Started: 2019-01-24

Compare observed Retention Time versus Sequence-specific calculated retention time using (F255744)
Comparizon | Session info | References
Rendered fromcompare-predicted-observed-flycodes.Rmdusingknitr::rmarkdown

Last update: 2019-01-24
Started: 2019-01-24