{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:1d7f029c-d6f9-4cb3-a280-b51ec80939b7",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-04484063v2",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "ImageJ",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"Fiji/ImageJ N/A https://imagej.net/software/fiji/",
"Fiji/ImageJ macro batch z projection N/A https://www.imperial.ac.uk/ medicine/facility-for-imaging- by-light-microscopy/software/fiji/ CellProfiler 4.0.7 (Stirling et al., 2021) 84 4.0.7 www.cellprofiler.org",
"DeboraOlivier/Telomere3D/ All Fiji/ImageJ (Schindelin et al., 2012) 83 & CellProfiler 4.0.7 (Stirling et al., 2021) 84 image analysis tools can be found at Pipelines for the BIP software are available online on Recherche Data Gouv INRAE https://doi.org/10.57745/",
"The intensity of the m6A signal was quantified using the ImageJ software.",
"Quality control on 3D-SIM images was done using different Fiji/ImageJ macros: first, images were thresholded in 16bit using a function within the SIMCheck plugin ( 34 , ''1_SIMCheck_THR_DKO.ijm'') then individual nuclei were cropped to ensure a single nucleus per image (''2_CropNucleiBoundingBox.ijm''), and finally the reconstruction quality was assessed via modulation contrast-to-noise ratio (MCNR) of SIMCheck, using a macro kindly provided by Lothar Schermelleh (''3_SIMCheck_QC_EzMiron.ijm''), both visually using the MCNR map on the image, and using the average value per image and channel."
]
}
}
{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:5ff803c9-6094-4612-913b-49bb9820e64c",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-03950358v1",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "Picard and Genome Analysis Toolkit (GATK",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"This file contained reads aligned to the human genome hg19 genome assembly (version b37, using BWA-MEM [version 0.7.15-r1140]) provided by the Picard and Genome Analysis Toolkit (GATK) developed at the Broad Institute , a process that involves marking duplicate reads, recalibrating base qualities and realigning around indels."
]
}
}
2026-04-05 06:44:07
urn:uuid:5e886fa9-e964-4c28-85eb-475e409f9975
https://datalake.inria.fr
https://inria.hal.science
["Offer","coar-notify:ReviewAction"]
{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:5e886fa9-e964-4c28-85eb-475e409f9975",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-03950358v1",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "CNVsingle",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"Thus CNVsingle provides allele-specific copy number profiles for all malignant cell clusters.",
"In brief, CNVsingle utilized normalization from matched PBMC derived B-cell profiles followed by Savitzky-Golay noise reduction.",
"Indeed, per CNVsingle, the intermediate state cells showed acquisition of early RSspecific events (i.e.",
"-We applied a novel tool CNVsingle (https://github.com/broadinstitute/CNVsingle) to the above processed Seurat objects.",
"Inferred allelic copy number from CNVsingle for each singlecell cluster (bottom) depicted adjacent to WES allelic copy number plots color-coded to show copy number events assigned to CLL and RS clones (Methods).",
"CODE AVAILABILITY STATEMENT Code is available for CNVsingle (https://github.com/broadinstitute/CNVsingle)",
"-We applied a novel tool CNVsingle (https://github.com/broadinstitute/CNVsingle) to the above processed Seurat objects.",
"-Expression analysis was performed on CLL and RS clusters identified as those CNVsingle profiles that matched the CLL WES or RS WES samples.",
"CODE AVAILABILITY STATEMENT Code is available for CNVsingle (https://github.com/broadinstitute/CNVsingle)"
]
}
}
2026-04-05 06:44:07
urn:uuid:59b48f8f-1ae0-4ca9-9fe6-48e9be807298
https://datalake.inria.fr
https://inria.hal.science
["Offer","coar-notify:ReviewAction"]
{
"@context": [
"https://www.w3.org/ns/activitystreams",
"https://purl.org/coar/notify"
],
"id": "urn:uuid:59b48f8f-1ae0-4ca9-9fe6-48e9be807298",
"type": [
"Offer",
"coar-notify:ReviewAction"
],
"actor": {
"id": "https://datalake.inria.fr",
"type": "Service",
"name": "Inria DataLake"
},
"origin": {
"id": "https://datalake.inria.fr",
"type": "Service",
"inbox": "https://prod-datadcis-api.inria.fr/coar/inbox"
},
"target": {
"id": "https://inria.hal.science",
"type": "Service",
"inbox": "https://inbox.hal.science"
},
"object": {
"id": "https://hal.science/hal-03950358v1",
"ietf:cite-as": null,
"sorg:citation": {
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"type": "SoftwareSourceCode",
"name": "ComBat-seq",
"codeRepository": null,
"referencePublication": null
},
"mentionType": "software",
"mentionContext": [
"RNA clustering of RS samples and integration with genetic subtypes-Gene counts were pre-processed with ComBat-seq (v3.42.0) to eliminate possible batch effects and one sample was removed as an outlier."
]
}
}