Abstract
Summary
HTSeq 2.0 provides a more extensive application programming interface including a new representation for sparse genomic data, enhancements for htseq-count to suit single-cell omics, ...a new script for data using cell and molecular barcodes, improved documentation, testing and deployment, bug fixes and Python 3 support.
Availability and implementation
HTSeq 2.0 is released as an open-source software under the GNU General Public License and is available from the Python Package Index at https://pypi.python.org/pypi/HTSeq. The source code is available on Github at https://github.com/htseq/htseq.
Supplementary information
Supplementary data are available at Bioinformatics online.
A search for the direct production of charginos and neutralinos in final states with at least two hadronically decaying tau leptons is presented. The analysis uses a dataset of pp collisions ...corresponding to an integrated luminosity of 36.1 fb−1 , recorded with the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 13 TeV. No significant deviation from the expected Standard Model background is observed. Limits are derived in scenarios of χ˜ + 1 χ˜ − 1 pair production and of χ˜ ± 1 χ˜ 0 2 and χ˜ + 1 χ˜ − 1 production in simplified models where the neutralinos and charginos decay solely via intermediate left-handed staus and tau sneutrinos, and the mass of the τ˜L state is set to be halfway between the masses of the χ˜ ± 1 and the χ˜ 0 1 . Chargino masses up to 630 GeV are excluded at 95% confidence level in the scenario of direct production of χ˜ + 1 χ˜ − 1 for a massless χ˜ 0 1 . Common χ˜ ± 1 and χ˜ 0 2 masses up to 760 GeV are excluded in the case of production of χ˜ ± 1 χ˜ 0 2 and χ˜ + 1 χ˜ − 1 assuming a massless χ˜ 0 1 . Exclusion limits for additional benchmark scenarios with large and small mass-splitting between the χ˜ ± 1 and the χ˜ 0 1 are also studied by varying the τ˜L mass between the masses of the χ˜ ± 1 and the χ˜ 0 1 .
Searches for the exclusive decays of the Higgs and Z bosons into a J/ψ, ψ(2S), or ϒ(nS) (n=1,2,3) meson and a photon are performed with a pp collision data sample corresponding to an integrated ...luminosity of 36.1fb−1 collected at s=13TeV with the ATLAS detector at the CERN Large Hadron Collider. No significant excess of events is observed above the expected backgrounds, and 95% confidence-level upper limits on the branching fractions of the Higgs boson decays to J/ψγ, ψ(2S)γ, and ϒ(nS)γ of 3.5×10−4, 2.0×10−3, and (4.9,5.9,5.7)×10−4, respectively, are obtained assuming Standard Model production. The corresponding 95% confidence-level upper limits for the branching fractions of the Z boson decays are 2.3×10−6, 4.5×10−6 and (2.8,1.7,4.8)×10−6, respectively.
A measurement of the Higgs boson production cross sections via associated WH and ZH production using H→WW⁎→ℓνℓν decays, where ℓ stands for either an electron or a muon, is presented. Results for ...combined WH and ZH production are also presented. The analysis uses events produced in proton–proton collisions collected with the ATLAS detector at the Large Hadron Collider in 2015 and 2016. The data correspond to an integrated luminosity of 36.1fb−1 recorded at a centre-of-mass energy of 13 TeV. The products of the H→WW⁎ branching fraction times the WH and ZH cross sections are measured to be 0.67−0.27+0.31(stat.)−0.14+0.18(syst.) pb and 0.54−0.24+0.31(stat.)−0.07+0.15(syst.) pb respectively, in agreement with the Standard Model predictions.
A search for the electroweak production of charginos and sleptons decaying into final states with two electrons or muons is presented. The analysis is based on 139 fb−1 of proton–proton collisions ...recorded by the ATLAS detector at the Large Hadron Collider at s√=13 TeV. Three R-parity-conserving scenarios where the lightest neutralino is the lightest supersymmetric particle are considered: the production of chargino pairs with decays via either W bosons or sleptons, and the direct production of slepton pairs. The analysis is optimised for the first of these scenarios, but the results are also interpreted in the others. No significant deviations from the Standard Model expectations are observed and limits at 95% confidence level are set on the masses of relevant supersymmetric particles in each of the scenarios. For a massless lightest neutralino, masses up to 420 GeV are excluded for the production of the lightest-chargino pairs assuming W-boson-mediated decays and up to 1 TeV for slepton-mediated decays, whereas for slepton-pair production masses up to 700 GeV are excluded assuming three generations of mass-degenerate sleptons.
The polarization of the Λ and ¯Λ hyperons along the beam (z) direction, Pz, has been measured in Pb-Pb collisions at √sNN=5.02 TeV recorded with ALICE at the Large Hadron Collider (LHC). The main ...contribution to Pz comes from elliptic flow-induced vorticity and can be characterized by the second Fourier sine coefficient Pz,s2=⟨Pzsin(2φ−2Ψ2)⟩, where φ is the hyperon azimuthal emission angle and Ψ2 is the elliptic flow plane angle. We report the measurement of Pz,s2 for different collision centralities and in the 30%–50% centrality interval as a function of the hyperon transverse momentum and rapidity. The Pz,s2 is positive similarly as measured by the STAR Collaboration in Au-Au collisions at √sNN=200 GeV, with somewhat smaller amplitude in the semicentral collisions. This is the first experimental evidence of a nonzero hyperon Pz in Pb-Pb collisions at the LHC. The comparison of the measured Pz,s2 with the hydrodynamic model calculations shows sensitivity to the competing contributions from thermal and the recently found shear-induced vorticity, as well as to whether the polarization is acquired at the quark-gluon plasma or the hadronic phase.
Inclusive ϒ(1S) and ϒ(2S) production have been measured in Pb–Pb collisions at the centre-of-mass energy per nucleon–nucleon pair sNN=5.02 TeV, using the ALICE detector at the CERN LHC. The ϒ mesons ...are reconstructed in the centre-of-mass rapidity interval 2.5<y<4 and in the transverse-momentum range pT<15 GeV/c, via their decays to muon pairs. In this Letter, we present results on the inclusive ϒ(1S) nuclear modification factor RAA as a function of collision centrality, transverse momentum and rapidity. The ϒ(1S) and ϒ(2S) RAA, integrated over the centrality range 0–90%, are 0.37±0.02(stat)±0.03(syst) and 0.10±0.04(stat)±0.02(syst), respectively, leading to a ratio RAAϒ(2S)/RAAϒ(1S) of 0.28±0.12(stat)±0.06(syst). The observed ϒ(1S) suppression increases with the centrality of the collision and no significant variation is observed as a function of transverse momentum and rapidity.
In this letter, the production of deuterons and anti-deuterons in pp collisions at s=7 TeV is studied as a function of the charged-particle multiplicity density at mid-rapidity with the ALICE ...detector at the LHC. Production yields are measured at mid-rapidity in five multiplicity classes and as a function of the deuteron transverse momentum (pT). The measurements are discussed in the context of hadron–coalescence models. The coalescence parameter B2, extracted from the measured spectra of (anti-)deuterons and primary (anti-)protons, exhibits no significant pT-dependence for pT<3GeV/c, in agreement with the expectations of a simple coalescence picture. At fixed transverse momentum per nucleon, the B2 parameter is found to decrease smoothly from low multiplicity pp to Pb–Pb collisions, in qualitative agreement with more elaborate coalescence models. The measured mean transverse momentum of (anti-)deuterons in pp is not reproduced by the Blast-Wave model calculations that simultaneously describe pion, kaon and proton spectra, in contrast to central Pb–Pb collisions. The ratio between the pT-integrated yield of deuterons to protons, d/p, is found to increase with the charged-particle multiplicity, as observed in inelastic pp collisions at different centre-of-mass energies. The d/p ratios are reported in a wide range, from the lowest to the highest multiplicity values measured in pp collisions at the LHC.
Azimuthal anisotropies of muons from charm and bottom hadron decays are measured in Pb+Pb collisions at sNN=5.02TeV. The data were collected with the ATLAS detector at the Large Hadron Collider in ...2015 and 2018 with integrated luminosities of 0.5nb−1 and 1.4nb−1, respectively. The kinematic selection for heavy-flavor muons requires transverse momentum 4<pT<30GeV and pseudorapidity |η|<2.0. The dominant sources of muons in this pT range are semi-leptonic decays of charm and bottom hadrons. These heavy-flavor muons are separated from light-hadron decay muons and punch-through hadrons using the momentum imbalance between the measurements in the tracking detector and in the muon spectrometers. Azimuthal anisotropies, quantified by flow coefficients, are measured via the event-plane method for inclusive heavy-flavor muons as a function of the muon pT and in intervals of Pb+Pb collision centrality. Heavy-flavor muons are separated into contributions from charm and bottom hadron decays using the muon transverse impact parameter with respect to the event primary vertex. Non-zero elliptic (v2) and triangular (v3) flow coefficients are extracted for charm and bottom muons, with the charm muon coefficients larger than those for bottom muons for all Pb+Pb collision centralities. The results indicate substantial modification to the charm and bottom quark angular distributions through interactions in the quark-gluon plasma produced in these Pb+Pb collisions, with smaller modifications for the bottom quarks as expected theoretically due to their larger mass.
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