HSeeker Contributors

7 files · 7.5 MB · gzip

Synthetic FASTA files used by the HSeeker benchmark suite (benchmarks/benchmark.py). Generated deterministically with fixed NumPy/Python random seeds documented in SEED_MANIFEST.json. Four sequence profiles: uniform (25 % each ACGT), ga_biased (90 % purine), ct_biased (90 % pyrimidine), realistic (~41 % GC). Two size tiers: small (~30 MB) and medium (~300 MB). Download via: python benchmarks/benchmark.py --from-zenodo

Kantor, Rose · Shakya, Migun · Ruth, Nelson · et al.

2,095 rows · 907 KB · fasta, tsv

A virus genome database representing 21,015 near-complete virus genomes collected from untargeted ultra-deep RNA/DNA combined sequencing of wastewater. Sequence data was provided by the CASPER consortium and raw data may be found on NCBI SRA under bioprojects PRJNA1247874 and PRJNA1198001. Data underwent read trimming, rRNA and human read removal, de novo assembly, and selection of high-quality viral contigs. Contigs were clustered at 95% identity and 85% query coverage to dereplicate. Chimera-checking required at least two independent assemblies of the same viral genome or presence of the genome in another reference database. Annotation made use of RdRpCATCH, geNomad, checkV, BLASTN against NCBI core-nt, and RNAVirHost. The RdRp fasta files contain representative RdRp sequences identified through homology to major RdRp reference databases and clustered at 90% sequence identity over 75% sequence coverage. Included sequences contain all three conserved RdRp motifs (A, B, and C) arranged in either the canonical ABC configuration or the permuted CAB configuration.

Robert Koch-Institut · AKTIN-Notaufnahmeregister

5 files · 10 KB · pdf, tsv, zip

Der Datensatz "Daten der Notaufnahmesurveillance" wird durch das Robert Koch-Institut und das AKTIN-Notaufnahmeregister bei Krankenhausaufnahmen bereitgestellt. Der Datensatz beinhaltet aggregierte Routinedaten aus deutschen Notaufnahmen zur syndromischen Überwachung von akuten Erkrankungen. Dazu zählen grippeähnliche Erkrankungen (ILI), Coronavirus-Erkrankungen (COVID-19), akute respiratorische Erkrankungen (ARE), gastrointestinale Infektionen (GI) und schwere akute respiratorische Infektionen (SARI). Dabei wird der relative Anteil dieser Erkrankungen an der Gesamtzahl der Notaufnahmevorstellungen sowie die berechneten Erwartungswerte und Prädiktionsintervalle ausgewiesen. Die Daten sind nach Notaufnahmetypen und Altersgruppen aggregiert. Damit bietet der Datensatz eine wertvolle Ressource für die Forschung im Bereich der Notfallmedizin und der Überwachung akuter Gesundheitsereignisse in Deutschland.

Computational Network Science

1 files · 415 KB · gzip

The drug-target-interaction dataset is a combinatorial complex representing drug-target interactions and similarity relationships. The dataset is based on the work by Perlman et al., which combines multiple drug and gene similarity measures to predict drug-target interactions. Find the dataset details in AHORN .

1 files · 29 KB · netcdf

NOAA Coral Reef Watch (v3.1 CoralTemp) Daily Global 5km Satellite Sea Surface Temperature Anomaly. This is a product of NOAA Coral Reef Watch Daily Global 5km Satellite Coral Bleaching Heat Stress Monitoring Product Suite cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature_anomaly (degree_C) mask (pixel characteristics flag array, pixel_classification)

1 files · 15 KB · netcdf

7-day average sea surface temperature (SST) from the AVHRR and VIIRS instruments aboard the NOAA and MetOp satellites, 2006-present, is generated by NOAA/NESDIS/STAR using the Advanced Clear-Sky Processor for Oceans (ACSPO) processing system. Only nighttime overpasses are used and composited into daily mean grids (~830 m), then the daily composite grids are averaged into gridded 7-day temperature averages. More info: https://eastcoast.coastwatch.noaa.gov/cw_avhrr-viirs_sst.php cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][level][latitude][longitude]): sst (sea_surface_subskin_temperature, degree_C)

1 files · 16 KB · netcdf

Climatological 7-day average sea surface temperature (SST) from 2007 to 2025, i.e. there are 52 7-day periods each representing a 2007-2025 mean SST for that period. The 18-year period for averaging begins May 21, 2007 and ends May 20, 2025. Data are merged from the AVHRR and VIIRS instruments aboard the NOAA and MetOp satellites. SST is generated by NOAA/NESDIS/STAR using the Advanced Clear-Sky Processor for Oceans (ACSPO) processing system. Only nighttime overpasses are used and composited into daily mean grids (~830 m), then the daily composite grids are averaged into gridded 7-day temperature averages. Finally, the 18-year climatological average for each 7-day period is averaged from the 7-day files. More info: https://eastcoast.coastwatch.noaa.gov/cw_avhrr-viirs_sst.php cdm_data_type = Grid VARIABLES (all of which use the dimensions [sevenDayPeriodOfYear][level][latitude][longitude]): sst (sea_surface_subskin_temperature, degree_C)

1 files · 16 KB · netcdf

Jet Propulsion Laboratory data from a local source. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][level][latitude][longitude]): sst (Analysed SST with land and ice masks applied, degree_C)

1 files · 15 KB · netcdf

Jet Propulsion Laboratory SST MUR data from a local source. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][level][latitude][longitude]): sst (Analysed SST with land and ice masks applied, degree_C)

1 files · 15 KB · netcdf

Jet Propulsion Laboratory data from a local source. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][level][latitude][longitude]): sst (Analysed SST with land and ice masks applied, degree_C)

1 files · 30 KB · netcdf

NOAA Coral Reef Watch Daily (v3.1) Global 5km Satellite Sea Surface Temperature (CoralTemp). CoralTemp is derived from three different but related 5km daily gap-free SST data sets and provides an internally consistent SST product that stretches from 1985 to present: Operational Sea Surface Temperature and Sea Ice Analysis (OSTIA) Sea Surface Temperature Reanalysis (1985-2002), Geo-Polar Blended Night-only Sea Surface Temperature Reanalysis (2002-2016), Geo-Polar Blended Night-only Sea Surface Temperature Near Real-Time (2017 to present). cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): analysed_sst (analysed sea surface temperature, degree_C) sea_ice_fraction (1)

1 files · 13 KB · netcdf

Sea surface temperature retrievals produced by NOAA/NESDIS/Office of Satellite and Product Operations (OSPO) office from Visible and Infrared Imager/Radiometer Suite (VIIRS) sensor cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][altitude][rows][cols]): l2p_flags swath_latitude (Latitude, degrees_north) swath_longitude (Longitude, degrees_east) sea_surface_temperature (sea surface subskin temperature, degree_C) sses_bias (SSES bias estimate, degree_C) sses_standard_deviation (degree_C) graphics (graphics overlay planes)

1 files · 17 KB · netcdf

Sea surface temperature retrievals produced by NOAA/NESDIS/STAR office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, degree_C) sses_bias (SSES bias estimate, kelvin) sses_standard_deviation (kelvin) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction (1) wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime (time difference of highest weighted input SST from reference time. Is equal to sst_dtime for pixels where L3S-LEO-PM_N is available, seconds) sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)

1 files · 17 KB · netcdf

Sea surface temperature retrievals produced by NOAA/NESDIS/STAR office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, kelvin) sses_bias (SSES bias estimate, kelvin) sses_standard_deviation (kelvin) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction (1) wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime (time difference of highest weighted input SST from reference time. Is equal to sst_dtime for pixels where L3S-LEO-PM_N is available, seconds) sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)

1 files · 17 KB · netcdf

Sea surface temperature retrievals produced by NOAA/NESDIS/STAR office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, kelvin) sses_bias (SSES bias estimate, kelvin) sses_standard_deviation (kelvin) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction (1) wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime (time difference of highest weighted input SST from reference time. Is equal to sst_dtime for pixels where L3S-LEO-PM_N is available, seconds) sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)

1 files · 40 KB · netcdf

Sea surface temperature retrievals produced by NOAA/NESDIS/OSPO office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, degree_C) sses_bias (SSES bias estimate, degree_C) sses_standard_deviation (degree_C) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)

1 files · 40 KB · netcdf

Sea surface temperature retrievals produced by NOAA/NESDIS/OSPO office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, degree_C) sses_bias (SSES bias estimate, degree_C) sses_standard_deviation (degree_C) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)

1 files · 17 KB · netcdf

Sea surface temperature retrievals produced by NOAA/NESDIS/STAR office cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (sea surface sub-skin temperature, degree_C) sses_bias (SSES bias estimate, degree_C) sses_standard_deviation (degree_C) l2p_flags l3s_flags sst_count (Count of input L3U SST pixels) quality_level (quality level of SST pixel) sst_source (Source of major (highest weight) contribution to sst) satellite_zenith_angle (degrees) dt_analysis (deviation from SST reference, kelvin) sea_ice_fraction (1) wind_speed (m s-1) sst_dtime (time difference from reference time, seconds) measurement_dtime (time difference of highest weighted input SST from reference time. Is equal to sst_dtime for pixels where L3S-LEO-PM_N is available, seconds) sst_gradient_magnitude (SST gradient magnitude value, kelvin/km) sst_front_position (Binary SST front position indicator)

1 files · 19 KB · netcdf

This is a product of NOAA Coral Reef Watch Global 5km Satellite Coral Bleaching Heat Stress Monitoring Product Suite, derived from CoralTemp v1.0. cdm_data_type = Grid VARIABLES (all of which use the dimensions [time][latitude][longitude]): sea_surface_temperature (analysed sea surface temperature, degree_C) mask (Pixel characteristics flag array, pixel_classification) sea_surface_temperature_anomaly (degree_C)