cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48370/ofd/b3eaha
title: Myodes glareolus - 22756, Zoological collection of the Mammal Research Institute, PAS

description: Myodes glareolus (Bank vole) from Zoological collection of the Mammal Research Institute, PAS. Collected 1959-07-25, in: Białowieża National Park, Poland. Material type:
DOI: 10.6084/m9.figshare.19845713.v1
title: Additional file 2 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 2: Table S1. QC metrics of genuine ChIP-seq data. Table of QC metrics of publicly available ChIP-seq datasets used for sub-sampling with DCSsub. The first six columns represent information on the original sample names, type (if genuine data or merged for subsequent sub-sampling), their peak shape, the replicate, and sample numbers and the regulation scenario in the original experiments respectively. The next columns show the total read number, the nonredundant read number, read length, and estimated fragment length. The QC metrics consist of the normalized strand coefficient (NSC) and the relative strand correlation (RSC) from cross-correlation analysis as signal-to-noise indicator, the background uniformity as a measure for peak reliability (by looking at the distribution of the mapped reads), and the fragment cluster score (FCS) for various strand shifts (read, fragment, 1k, 10k and 100k) to identify peak mode and intensity.
DOI: 10.6084/m9.figshare.19845716
title: Additional file 3 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 3: Table S2. Benchmarked DCS tools. Table of DCS tools, their focus, platform / programming language, version used, peak dependence, ease of installation, publication, number of citations (Google Scholar 2019-11-28), and the link to the respective website or download location. Ease of installation: +++ : Execution of a few predefined lines, including all tools that can be installed via Bioconductor and pip. Installation time, seconds-minutes. ++ : Compilation/manual installation of requirements. Installation time, minutes. + : Compilation and manual installation of requirements. Installation time, minutes-hours. - : Manual compilation/installation of source code and requirements or modification in source code required. Installation time, hours-days.
DOI: 10.6084/m9.figshare.19845716.v1
title: Additional file 3 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 3: Table S2. Benchmarked DCS tools. Table of DCS tools, their focus, platform / programming language, version used, peak dependence, ease of installation, publication, number of citations (Google Scholar 2019-11-28), and the link to the respective website or download location. Ease of installation: +++ : Execution of a few predefined lines, including all tools that can be installed via Bioconductor and pip. Installation time, seconds-minutes. ++ : Compilation/manual installation of requirements. Installation time, minutes. + : Compilation and manual installation of requirements. Installation time, minutes-hours. - : Manual compilation/installation of source code and requirements or modification in source code required. Installation time, hours-days.
DOI: 10.6084/m9.figshare.19845722
title: Additional file 5 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 5: Table S4. DCS scores. Table of test scenarios, DCS tools, applied peak caller and parameters, AUPRC values, the scaled runtime and preparation time, scaled memory usage, scaled number of NAs and standard deviation, and the DCS score.
DOI: 10.6084/m9.figshare.19845722.v1
title: Additional file 5 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 5: Table S4. DCS scores. Table of test scenarios, DCS tools, applied peak caller and parameters, AUPRC values, the scaled runtime and preparation time, scaled memory usage, scaled number of NAs and standard deviation, and the DCS score.
DOI: 10.6084/m9.figshare.19845725.v1
title: Additional file 6 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 6: Table S5. DCS scores per peak and regulation scenario. Table of DCS score ranked DCS tools, the applied peak caller and parameter setup, and the DCS score for: all test sets averaged, the 50:50, and 100:0 regulation scenarios, TF, sharp mark, and broad mark peak shapes, and all combinations of regulation scenario, and peak shape: TF 50:50, TF 100:0, sharp mark 50:50, sharp mark 100:0, broad mark 50:50, and broad mark 100:0.
DOI: 10.34808/1543-hn86
title: Malignant neoplasm of unspecified ovary - Female, 66 - Tissue image [9020730024811511]

description: This is the histopathological image of RETROPERITONEUM AND PERITONEUM tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 66Clinical description: Tumour of the omentumGender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter II - NeoplasmsDiagnosis: Malignant neoplasm of unspecified ovaryResult of the histopathological examination: High grade serous adenocarcinoma  (G3) infiltrating the omentum.Sample:Material: FFPECollecting method: Surgical specimenTopography: RETROPERITONEUM AND PERITONEUMOrgan: RETROPERITONEUM AND PERITONEUMTissue: OmentumType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.6084/m9.figshare.19845719
title: Additional file 4 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 4: Table S3. Applied parameter setups per DCS tool and peak caller. Table describing DCS tools, peak caller and the random classifier by their name, peak dependence, parameter setup name, if a scaling factor was used, setup description, and setup parameter details for the essential core steps.
DOI: 10.6084/m9.figshare.19845719.v1
title: Additional file 4 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 4: Table S3. Applied parameter setups per DCS tool and peak caller. Table describing DCS tools, peak caller and the random classifier by their name, peak dependence, parameter setup name, if a scaling factor was used, setup description, and setup parameter details for the essential core steps.
DOI: 10.6084/m9.figshare.19845725
title: Additional file 6 of Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection

description: Additional file 6: Table S5. DCS scores per peak and regulation scenario. Table of DCS score ranked DCS tools, the applied peak caller and parameter setup, and the DCS score for: all test sets averaged, the 50:50, and 100:0 regulation scenarios, TF, sharp mark, and broad mark peak shapes, and all combinations of regulation scenario, and peak shape: TF 50:50, TF 100:0, sharp mark 50:50, sharp mark 100:0, broad mark 50:50, and broad mark 100:0.
DOI: 10.34808/rzk3-ps74
title: Endometrioid adenocarcinoma, NOS - Female, 75 - Tissue image [4100730020128291]

description: This is the histopathological image of CORPUS UTERI tissue sample obtained in University of Warmia and Mazury in Olsztyn and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 75Clinical description: Vaginal bleeding.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: ADENOMAS AND ADENOCARCINOMASDiagnosis: Endometrioid adenocarcinoma, NOSResult of the histopathological examination: Endometrioid adenocarcinoma of the uterus G2.Sample:Material: FFPECollecting method: Surgical specimenTopography: FEMALE GENITAL ORGANSOrgan: CORPUS UTERITissue: Body of uterusType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: University of Warmia and Mazury in Olsztyn
DOI: 10.34808/sc2c-5p75
title: Squamous cell carcinoma, NOS - Female, 71 - Tissue image [3280730025625341]

description: This is the histopathological image of CERVIX UTERI tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 71Clinical description: HSIL in the cervical biopsy.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: SQUAMOUS CELL NEOPLASMSDiagnosis: Squamous cell carcinoma, NOSResult of the histopathological examination: HSIL with foci of microinvasion. IHC: p16+, p53+.Sample:Material: FFPECollecting method: Surgical biopsyTopography: FEMALE GENITAL ORGANSOrgan: CERVIX UTERITissue: External osType of staining: positive/IHCStaining: Not applicableAntibody: p53Technology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.48370/ofd/4ialxc
title: Myodes glareolus - 34581, Zoological collection of the Mammal Research Institute, PAS

description: Myodes glareolus (Bank vole) from Zoological collection of the Mammal Research Institute, PAS. Collected 1964-01-17, in: Białowieża National Park, Poland. Material type:
DOI: 10.34808/67z4-cz80
title: Invasive breast carcinoma of no special type - Female, 40 - Tissue image [523073001328171]

description: This is the histopathological image of BREAST tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: VS200 Olympus slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 40Clinical description: Breast cancer after chemotherapy.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: DUCTAL AND LOBULAR NEOPLASMSDiagnosis: Invasive breast carcinoma of no special typeResult of the histopathological examination: fragment of breast tissue after neoadjuvant chemotherapy with features of fibrosclerotic and cystic lesions, with the presence of few microcalcifications and atrophy of the glands.Sample:Material: FFPECollecting method: Surgical specimenTopography: BREASTOrgan: BREASTTissue: Central portion of breastType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: VS200 OlympusLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.48370/ofd/qyk8gj/6bl5zn
title: m-2753.tif

description: :unav
DOI: 10.34808/8akn-b026
title: Synovial sarcoma, NOS - Female, 20 - Tissue image [3150630013128431]

description: This is the histopathological image of CONNECTIVE, SUBCUTANEOUS AND OTHER SOFT TISSUES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 20Clinical description: Tumor of left upper limb.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: SYNOVIAL-LIKE NEOPLASMSDiagnosis: Synovial sarcoma, NOSResult of the histopathological examination: Synovial sarcoma: VIM+, EMA focally+, CD99+, CD56+, CKAE1/AE3-, S100-, CD34-, SMA-, HMB45-, Ki-67 30%. 
(FISH: presence of SS18 rearrangement).Sample:Material: FFPECollecting method: Surgical biopsyTopography: CONNECTIVE, SUBCUTANEOUS AND OTHER SOFT TISSUESOrgan: CONNECTIVE, SUBCUTANEOUS AND OTHER SOFT TISSUESTissue: Connective, subcutaneous and other soft tissues of upper limb and shoulderType of staining: positive/IHCStaining: Not applicableAntibody: Ki-67Technology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/0w29-dz07
title: Hurthle cell carcinoma - Not available, 65 - Tissue image [3300730069479201]

description: This is the histopathological image of THYROID GLAND tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 65Clinical description: A thyroid lobe measuring 5.5x4x4 cm. An ill-defined, beige tumor measuring approximately 4.4x2.8x2 cm was present on sectioning.Gender: Not availableDiagnosis:Classification: ICD-O_3.2Classification code: ADENOMAS AND ADENOCARCINOMASDiagnosis: Hurthle cell carcinomaResult of the histopathological examination: Hurtle cell carcinoma, widely invasive. Tumor confined to the thyroid gland removed completely. Features of angioinvasion in single blood vessels at the periphery of the tumor are present. IHC: calcitonin(-), synaptophysin (-/+), chromogranin A(-), TTF1(+), Ki67 10%. Mitotic figures: 1/10 HPF.Sample:Material: FFPECollecting method: Surgical specimenTopography: THYROID AND OTHER ENDOCRINE GLANDSOrgan: THYROID GLANDTissue: Thyroid, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/9yg8-v177
title: Seminoma, NOS - Male, 33 - Tissue image [5020730020706371]

description: This is the histopathological image of TESTIS tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 33Clinical description: 2 months history of tumor of left testis. Hypoechoic well-circumscribed tumor on ultrasound.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: GERM CELL NEOPLASMSDiagnosis: Seminoma, NOSResult of the histopathological examination: Seminoma of testis. Intratubular seminoma. Germ cell neoplasia in situ. Epididymis without seminoma infiltration. Leydig cells hyperplasia in testis parenchyma.Sample:Material: FFPECollecting method: Surgical specimenTopography: MALE GENITAL ORGANSOrgan: TESTISTissue: Testis, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.48370/ofd/qyk8gj/onypxg
title: FMW Antrodia sinuosa (Fries) P. Karsten M-2753.JPG

description: :unav
DOI: 10.48370/ofd/qyk8gj/joalug
title: FMW Antrodia sinuosa (Fries) P. Karsten M-2753 (2).JPG

description: :unav
DOI: 10.34808/enna-h208
title: Neurofibroma, NOS - Female, 13 - Tissue image [5070730026201181]

description: This is the histopathological image of CONNECTIVE, SUBCUTANEOUS AND OTHER SOFT TISSUES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 13Clinical description: Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: NERVE SHEATH TUMORSDiagnosis: Neurofibroma, NOSResult of the histopathological examination: Sample:Material: FFPECollecting method: Surgical biopsyTopography: CONNECTIVE, SUBCUTANEOUS AND OTHER SOFT TISSUESOrgan: CONNECTIVE, SUBCUTANEOUS AND OTHER SOFT TISSUESTissue: Connective, subcutaneous and other soft tissues of head, face, and neckType of staining: positive/IHCStaining: Not applicableAntibody: s100Technology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.48370/ofd/tvik0v
title: Myodes glareolus - 162984, Zoological collection of the Mammal Research Institute, PAS

description: Myodes glareolus (Bank vole) from Zoological collection of the Mammal Research Institute, PAS. Collected 1993-09-29, in: Białowieża National Park, Poland. Material type:
DOI: 10.34808/1knz-5p81
title: Hyperplasia of prostate - Male, 77 - Tissue image [5160730021354261]

description: This is the histopathological image of PROSTATE GLAND tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 77Clinical description: No clinical data.Gender: MaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter XIV - Diseases of the genitourinary systemDiagnosis: Hyperplasia of prostateResult of the histopathological examination: Benign prostatic hyperplasia (BPH).Sample:Material: FFPECollecting method: Surgical specimenTopography: MALE GENITAL ORGANSOrgan: PROSTATE GLANDTissue: Prostate, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.48370/ofd/qyk8gj
title: Jamkówka pogięta (Antrodia sinuosa (Fries) P. Karsten), 2753

description: Grzyby makromycetes
DOI: 10.34808/besg-x445
title: Phyllodes tumor, benign - Female, 55 - Tissue image [8100730018743911]

description: This is the histopathological image of BREAST tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 55Clinical description: Palpable 3 cm tumor of left breast.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: FIBROEPITHELIAL NEOPLASMSDiagnosis: Phyllodes tumor, benignResult of the histopathological examination: Benign phyllodes tumor.Sample:Material: FFPECollecting method: Surgical specimenTopography: BREASTOrgan: BREASTTissue: Upper-outer quadrant of breastType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/28j4-p118
title: Cystosarcoma phyllodes, benign - Female, 70 - Tissue image [8100730018756211]

description: This is the histopathological image of BREAST tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 70Clinical description: Enlarged left breast. 29 x 16 mm well-circumscribed solid hypoechoic tumor on ultrasound. Suspicion of phyllodes tumor. 
Core needle biopsy: fibroadenoma.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: FIBROEPITHELIAL NEOPLASMSDiagnosis: Cystosarcoma phyllodes, benignResult of the histopathological examination: Benign phyllodes tumor.Sample:Material: FFPECollecting method: Surgical specimenTopography: BREASTOrgan: BREASTTissue: Upper-outer quadrant of breastType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.48370/ofd/832eni
title: Myodes glareolus - 158555, Zoological collection of the Mammal Research Institute, PAS

description: Myodes glareolus (Bank vole) from Zoological collection of the Mammal Research Institute, PAS. Collected 1989-09-22, in: Białowieża National Park, Poland. Material type:
DOI: 10.6084/m9.figshare.19682400
title: Tribolium freemani genome assembly annotations

description: Dataset containing all genetic and assembly features of Tribolium freemani genome (Tfree1.0).
DOI: 10.34808/nffd-9g74
title: Mesoblastic nephroma - Male, 1 - Tissue image [5040730028023911]

description: This is the histopathological image of KIDNEY tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 1Clinical description: Tumor of the kidney.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: COMPLEX MIXED AND STROMAL NEOPLASMSDiagnosis: Mesoblastic nephromaResult of the histopathological examination: Mesoblastic nephroma. IHC: CK AE1/3 (-), vimentin (+), WT 1- cytoplasmic reaction, CD 56 +, p53-, SMA+, desmin (-), synaptophysin (-), CD 99 (+), NSE (-), bcl 2 +/-, cyclin D1 (+), PAX 8 (-), EMA (-), CD 34 (-), Pan TRK (-)).Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: KIDNEYTissue: Kidney, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/3fct-gt03
title: Mild cervical dysplasia - Female, 38 - Tissue image [4090730013126931]

description: This is the histopathological image of CERVIX UTERI tissue sample obtained in University of Warmia and Mazury in Olsztyn and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 38Clinical description: HSIL in the pap smear.Gender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter XIV - Diseases of the genitourinary systemDiagnosis: Mild cervical dysplasiaResult of the histopathological examination: LSIL (CIN1).Sample:Material: FFPECollecting method: Surgical specimenTopography: FEMALE GENITAL ORGANSOrgan: CERVIX UTERITissue: ExocervixType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: University of Warmia and Mazury in Olsztyn
DOI: 10.48370/ofd/l01rq4
title: Myodes glareolus - 160306, Zoological collection of the Mammal Research Institute, PAS

description: Myodes glareolus (Bank vole) from Zoological collection of the Mammal Research Institute, PAS. Collected 1990-09-23, in: Białowieża National Park, Poland. Material type:
DOI: 10.34808/76hf-hg41
title: Melanoma, metastatic - Male, 68 - Tissue image [11020630022697661]

description: This is the histopathological image of LIVER AND INTRAHEPATIC BILE DUCTS tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 68Clinical description: History of melanoma of eyeball. CT: numerous tumors in liver, suspicion of metastases.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: NEVI AND MELANOMASDiagnosis: Melanoma, metastaticResult of the histopathological examination: Metastasis of melanoma to liver.Sample:Material: FFPECollecting method: Surgical specimenTopography: DIGESTIVE ORGANSOrgan: LIVER AND INTRAHEPATIC BILE DUCTSTissue: LiverType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk