Datasets:
Tasks:
Other
Formats:
csv
Languages:
English
Size:
< 1K
Tags:
🧬 genomics
📊 bigwig / functional tracks
🎯 regression
⚡ fine-tuning
🧪 sequence-to-signal
📐 functional-genomics
License:
| language: | |
| - en | |
| pretty_name: "NTv3 tutorial dataset - Genome & functional tracks" | |
| tags: | |
| - 🧬 genomics | |
| - 📊 bigwig / functional tracks | |
| - 🎯 regression | |
| - ⚡ fine-tuning | |
| - 🧪 sequence-to-signal | |
| - 📐 functional-genomics | |
| - 🔬 bioinformatics | |
| task_categories: | |
| - other | |
| size_categories: | |
| - 100K<n<1M | |
| license: cc-by-nc-4.0 | |
| # NTv3 Benchmark Dataset | |
| This dataset contains the functional tracks and genome annotations used in the NTv3 benchmark evaluation. | |
| ## Dataset Organization | |
| The dataset is organized as follows: | |
| ``` | |
| InstaDeepAI/NTv3_benchmark_dataset/ | |
| ├── <species>/ | |
| │ ├── functional_tracks/ | |
| │ │ ├── <track_name>.bigwig | |
| │ │ └── ... | |
| │ └── genome_annotation/ | |
| │ ├── <track_name>.bed | |
| │ └── ... | |
| ``` | |
| ## Available Species | |
| - **arabidopsis** | |
| - **chicken** | |
| - **cattle** | |
| - **human** | |
| - **maize** | |
| - **rice** | |
| - **tomato** | |
| ## Downloading Files | |
| You can download files directly using their URLs: | |
| ```python | |
| from huggingface_hub import hf_hub_download | |
| import requests | |
| # Download a BigWig file | |
| bigwig_path = hf_hub_download( | |
| repo_id="InstaDeepAI/NTv3_benchmark_dataset", | |
| filename="human/functional_tracks/ENCSR628PLS.bigwig", | |
| repo_type="dataset" | |
| ) | |
| # Download a BED file | |
| bed_path = hf_hub_download( | |
| repo_id="InstaDeepAI/NTv3_benchmark_dataset", | |
| filename="human/genome_annotation/exon.bed", | |
| repo_type="dataset" | |
| ) | |
| ``` | |
| ### Direct URL Access | |
| You can also construct direct URLs to download files: | |
| ```python | |
| import requests | |
| # Construct URL | |
| base_url = 'https://huggingface.co/datasets/InstaDeepAI/NTv3_benchmark_dataset/resolve/main' | |
| file_path = "human/functional_tracks/ENCSR628PLS.bigwig" | |
| url = f"{base_url}/{file_path}" | |
| # Download file | |
| response = requests.get(url) | |
| with open("local_file.bigwig", "wb") as f: | |
| f.write(response.content) | |
| ``` | |
| ## Available Tracks | |
| ### Human | |
| #### Functional Tracks | |
| Files are named by their S3 track ID (file_id). The mapping from track ID to track description can be found in the benchmark documentation. | |
| - `human/functional_tracks/ENCSR628PLS.bigwig` (GM18861_chromatin_accessibility) | |
| - `human/functional_tracks/ENCSR487QSB.bigwig` (GM18907_chromatin_accessibility) | |
| - `human/functional_tracks/ENCSR410DWV.bigwig` (motor_neuron_chromatin_accessibility) | |
| - `human/functional_tracks/ENCSR325NFE.bigwig` (bile_duct_chromatin_accessibility) | |
| - `human/functional_tracks/ENCSR814RGG.bigwig` (ureter_chromatin_accessibility) | |
| - `human/functional_tracks/ENCSR863PSM.bigwig` (BLaER1_H3K4me1) | |
| - `human/functional_tracks/ENCSR682BFG.bigwig` (motor_neuron_H3K4me1) | |
| - `human/functional_tracks/ENCSR754DRC.bigwig` (motor_neuron_H3K27ac) | |
| - `human/functional_tracks/ENCSR962OTG.bigwig` (motor_neuron_H3K4me3) | |
| - `human/functional_tracks/ENCSR046BCI_M.bigwig` (A673_PROcap_minus) | |
| - `human/functional_tracks/ENCSR046BCI_P.bigwig` (A673_PROcap_plus) | |
| - `human/functional_tracks/ENCSR100LIJ_M.bigwig` (Caco-2_PROcap_minus) | |
| - `human/functional_tracks/ENCSR100LIJ_P.bigwig` (Caco-2_PROcap_plus) | |
| - `human/functional_tracks/ENCSR935RNW_M.bigwig` (Calu3_PROcap_minus) | |
| - `human/functional_tracks/ENCSR935RNW_P.bigwig` (Calu3_PROcap_plus) | |
| - `human/functional_tracks/ENCSR114HGS_M.bigwig` (K562_PROcap_minus) | |
| - `human/functional_tracks/ENCSR114HGS_P.bigwig` (K562_PROcap_plus) | |
| - `human/functional_tracks/ENCSR799DGV_M.bigwig` (MCF10A_PROcap_minus) | |
| - `human/functional_tracks/ENCSR799DGV_P.bigwig` (MCF10A_PROcap_plus) | |
| - `human/functional_tracks/ENCSR154HRN_M.bigwig` (K562_HNRNPA1_eCLIP_minus) | |
| - `human/functional_tracks/ENCSR154HRN_P.bigwig` (K562_HNRNPA1_eCLIP_plus) | |
| - `human/functional_tracks/ENCSR249ROI_M.bigwig` (K562_HNRNPC_eCLIP_minus) | |
| - `human/functional_tracks/ENCSR249ROI_P.bigwig` (K562_HNRNPC_eCLIP_plus) | |
| - `human/functional_tracks/ENCSR321PWZ_M.bigwig` (K562_SRSF1_eCLIP_minus) | |
| - `human/functional_tracks/ENCSR321PWZ_P.bigwig` (K562_SRSF1_eCLIP_plus) | |
| - `human/functional_tracks/ENCSR484LTQ_M.bigwig` (K562_NCBP2_eCLIP_minus) | |
| - `human/functional_tracks/ENCSR484LTQ_P.bigwig` (K562_NCBP2_eCLIP_plus) | |
| - `human/functional_tracks/ENCSR862QCH_M.bigwig` (K562_U2AF1_eCLIP_minus) | |
| - `human/functional_tracks/ENCSR862QCH_P.bigwig` (K562_U2AF1_eCLIP_plus) | |
| - `human/functional_tracks/ENCSR527JGN_M.bigwig` (BLaER1_gene_expression_minus) | |
| - `human/functional_tracks/ENCSR527JGN_P.bigwig` (BLaER1_gene_expression_plus) | |
| - `human/functional_tracks/ENCSR701YIC.bigwig` (motor_neuron_gene_expression) | |
| - `human/functional_tracks/ENCSR619DQO_M.bigwig` (ureter_gene_expression_minus) | |
| - `human/functional_tracks/ENCSR619DQO_P.bigwig` (ureter_gene_expression_plus) | |
| #### Genome Annotations | |
| - `human/genome_annotation/exon.bed` (exon) | |
| - `human/genome_annotation/intron.bed` (intron) | |
| - `human/genome_annotation/splice_acceptor.bed` (splice_acceptor) | |
| - `human/genome_annotation/start_codon.bed` (start_codon) | |
| ### Chicken | |
| #### Functional Tracks | |
| - `chicken/functional_tracks/ERX9662174.bigwig` (bone_marrow_chromatin_accessibility) | |
| - `chicken/functional_tracks/ERX9662188.bigwig` (bone_marrow_gene_expression) | |
| - `chicken/functional_tracks/ERX9662177.bigwig` (heart_chromatin_accessibility) | |
| - `chicken/functional_tracks/ERX9662190.bigwig` (heart_gene_expression) | |
| - `chicken/functional_tracks/ERX9662178.bigwig` (kidney_chromatin_accessibility) | |
| - `chicken/functional_tracks/ERX9662192.bigwig` (kidney_gene_expression) | |
| - `chicken/functional_tracks/ERX9662183.bigwig` (testis_chromatin_accessibility) | |
| - `chicken/functional_tracks/ERX9662196.bigwig` (testis_gene_expression) | |
| - `chicken/functional_tracks/ERX9662185.bigwig` (thymus_chromatin_accessibility) | |
| - `chicken/functional_tracks/ERX9662198.bigwig` (thymus_gene_expression) | |
| - `chicken/functional_tracks/ERX9662186.bigwig` (trachea_chromatin_accessibility) | |
| - `chicken/functional_tracks/ERX9662200.bigwig` (trachea_gene_expression) | |
| - `chicken/functional_tracks/ERX9662180.bigwig` (uterus_chromatin_accessibility) | |
| - `chicken/functional_tracks/ERX9662194.bigwig` (uterus_gene_expression) | |
| ### Arabidopsis | |
| #### Functional Tracks | |
| - `arabidopsis/functional_tracks/SRR13808079.bigwig` (flower_mature_riboseq) | |
| - `arabidopsis/functional_tracks/SRR13808080.bigwig` (flower_mature_riboseq_2) | |
| - `arabidopsis/functional_tracks/SRR13808081.bigwig` (fruit_mature_riboseq) | |
| - `arabidopsis/functional_tracks/SRR13808084.bigwig` (root_mature_riboseq) | |
| ### Rice | |
| #### Functional Tracks | |
| - `rice/functional_tracks/SRR13808064.bigwig` (leaf_V2_stage_riboseq) | |
| - `rice/functional_tracks/SRR13808065.bigwig` (leaf_V2_stage_riboseq_2) | |
| - `rice/functional_tracks/SRR13808066.bigwig` (leaf_booting_stage_riboseq_2) | |
| - `rice/functional_tracks/SRR13808067.bigwig` (leaf_booting_stage_riboseq) | |
| - `rice/functional_tracks/SRR13808068.bigwig` (root_V2_stage_riboseq) | |
| - `rice/functional_tracks/SRR13808069.bigwig` (seedling_V2_stage_riboseq) | |
| - `rice/functional_tracks/SRR13808070.bigwig` (sheath_V2_stage_riboseq) | |
| - `rice/functional_tracks/SRR13808072.bigwig` (sheath_V2_stage_riboseq_2) | |
| - `rice/functional_tracks/SRR13808073.bigwig` (sheath_booting_stage_riboseq) | |
| - `rice/functional_tracks/SRR13808074.bigwig` (sheath_booting_stage_riboseq_2) | |
| - `rice/functional_tracks/SRR13808075.bigwig` (spikelet_booting_stage_riboseq) | |
| - `rice/functional_tracks/SRR13808076.bigwig` (spikelet_booting_stage_riboseq_2) | |
| - `rice/functional_tracks/SRR13808077.bigwig` (stem_booting_stage_riboseq) | |
| - `rice/functional_tracks/SRR13808078.bigwig` (stem_booting_stage_riboseq_2) | |
| ### Maize | |
| #### Functional Tracks | |
| - `maize/functional_tracks/SRR13808051.bigwig` (ear_V12_stage_riboseq) | |
| - `maize/functional_tracks/SRR13808052.bigwig` (ear_V12_stage_riboseq_2) | |
| - `maize/functional_tracks/SRR13808056.bigwig` (root_14days_riboseq) | |
| - `maize/functional_tracks/SRR13808058.bigwig` (seedling_14days_riboseq) | |
| - `maize/functional_tracks/SRR13808059.bigwig` (stem_14days_riboseq) | |
| - `maize/functional_tracks/SRR13808061.bigwig` (stem_14days_riboseq_2) | |
| - `maize/functional_tracks/SRR13808062.bigwig` (tassel_V12_stage_riboseq) | |
| - `maize/functional_tracks/SRR13808063.bigwig` (tassel_V12_stage_riboseq_2) | |
| ### Tomato | |
| #### Functional Tracks | |
| - `tomato/functional_tracks/SRX27799703.bigwig` (fruit_0DPA_chromatin_accessibility) | |
| - `tomato/functional_tracks/SRX29291440.bigwig` (fruit_0DPA_MicroTom_gene_expression) | |
| - `tomato/functional_tracks/SRX29291439.bigwig` (fruit_0DPA_MicroTom_gene_expression_2) | |
| - `tomato/functional_tracks/SRX29291438.bigwig` (fruit_0DPA_MicroTom_gene_expression_3) | |
| - `tomato/functional_tracks/SRX27799731.bigwig` (fruit_10DPA_chromatin_accessibility) | |
| - `tomato/functional_tracks/SRX29291448.bigwig` (fruit_10DPA_MicroTom_gene_expression) | |
| - `tomato/functional_tracks/SRX29291447.bigwig` (fruit_10DPA_MicroTom_gene_expression_2) | |
| - `tomato/functional_tracks/SRX29291446.bigwig` (fruit_10DPA_MicroTom_gene_expression_3) | |
| - `tomato/functional_tracks/SRX29291431.bigwig` (fruit_15DPA_MicroTom_gene_expression) | |
| - `tomato/functional_tracks/SRX29291430.bigwig` (fruit_15DPA_MicroTom_gene_expression_2) | |
| - `tomato/functional_tracks/SRX29291445.bigwig` (fruit_15DPA_Wild_LA1781_gene_expression) | |
| - `tomato/functional_tracks/SRX29291442.bigwig` (fruit_15DPA_Wild_LA1781_gene_expression_2) | |
| - `tomato/functional_tracks/SRX27799722.bigwig` (fruit_3DBA_chromatin_accessibility) | |
| - `tomato/functional_tracks/SRX27799719.bigwig` (fruit_3DPA_chromatin_accessibility) | |
| - `tomato/functional_tracks/SRX27799727.bigwig` (fruit_5DPA_chromatin_accessibility) | |
| - `tomato/functional_tracks/SRX29291444.bigwig` (fruit_5DPA_MicroTom_gene_expression) | |
| - `tomato/functional_tracks/SRX29291443.bigwig` (fruit_5DPA_MicroTom_gene_expression_2) | |
| - `tomato/functional_tracks/SRX29291441.bigwig` (fruit_5DPA_MicroTom_gene_expression_3) | |
| - `tomato/functional_tracks/SRX27799718.bigwig` (fruit_7DPA_chromatin_accessibility) | |
| - `tomato/functional_tracks/SRX27799733.bigwig` (leaf_chromatin_accessibility) | |
| #### Genome Annotations | |
| - `tomato/genome_annotation/exon.bed` (exon) | |
| - `tomato/genome_annotation/intron.bed` (intron) | |
| - `tomato/genome_annotation/splice_acceptor.bed` (splice_acceptor) | |
| - `tomato/genome_annotation/start_codon.bed` (start_codon) | |
| ### Cattle | |
| #### Genome Annotations | |
| - `cattle/genome_annotation/exon.bed` (exon) | |
| - `cattle/genome_annotation/intron.bed` (intron) | |
| - `cattle/genome_annotation/splice_acceptor.bed` (splice_acceptor) | |
| - `cattle/genome_annotation/start_codon.bed` (start_codon) | |
| ## Track Information | |
| ### Functional Tracks | |
| Functional tracks include: | |
| - Chromatin Accessibility tracks | |
| - Histone modifications (H3K4me1, H3K4me3, H3K27ac) | |
| - Transcription initiation (PRO-cap) | |
| - RNA binding sites (eCLIP) | |
| - Gene Expression | |
| - mRNA translation (Ribo-seq) | |
| ### Genome Annotations | |
| Genome annotation tracks include: | |
| - Exon | |
| - Intron | |
| - Splice Acceptor | |
| - Start Codon | |
| ## Notes | |
| - BigWig files can be read using libraries like `pyBigWig` | |
| - BED files can be read using `pyranges` or `pandas` | |
| - All tracks are in the same coordinate system as specified in the benchmark | |