The 29-year-old, an author and journalist from Belfast, died at Altnagelvin hospital after being wounded in the Creggan area.
During the disturbances, more than 50 petrol bombs were thrown at police and two cars were hijacked and set ablaze.
The force's Assistant Chief Constable Mark Hamilton called the killing a "horrendous act", carried out by people that "do not care who they harm".
Hours before her death she tweeted a photo of the riot with the words: "Derry tonight".
The New IRA is a small group who reject the 1998 Good Friday agreement that marked the Irish Republican Army's embrace of a political solution to the long-running violence known as "The Troubles" that claimed more than 3,700 lives.
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Republican political party Saoradh said a "republican volunteer" was trying to "defend people" from the police late Thursday when the shot was sacked that "accidentally" hit McKee.
The Police Service of Northern Ireland said officers took the adolescents, ages 18 and 19 into custody under its anti-terrorism laws.
Her partner, Sara Canning, told a vigil Friday that McKee's wonderful potential had been snuffed out.
The partner of a 29-year-old journalist who was shot dead during riots in Derry last night has said her legacy will "live on in the light that she has left behind". "We believe that dissident republicans have a number of attacks planned and we assess it is likely that these would have been used over the Easter period", Hamilton said.
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Afternoon temperatures will range from 15 or 16 degrees in the northwest to between 17 and 22 degrees elsewhere. Met Eireann says that latest indications suggest breezier generally on Monday especially on the west coast.
The detective leading the Lyra McKee murder investigation has said he believes the perpetrators were from the New IRA.
"It has left so many friends without their confidante", she added. The city was the scene of a vehicle bombing in January, in a suspected attack by the New IRA.
There has been an increase in tensions in Northern Ireland in recent months with sporadic violence, much of it focused in Londonderry, also known as Derry. McKee's death is being treated as a terrorist incident.
Police at the scene of a shooting in Derry, Northern Ireland. She grew up in a Catholic neighborhood of Belfast, the Times reports, and wrote movingly about her experiences as a gay woman and a member of Northern Ireland's post-cease-fire generation. Lyra was a bright, intelligent and articulate writer with a witty, warm and fun loving personality and her murder has sent shock waves among the entire community.
"You have robbed her partner of their life together, and her family".
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Brind'Amour said he was treated and evaluated at the hospital. "He has a special bond with our group, with me too". Limiting Washington to just one shot throughout the period, the Hurricanes were firmly in control at that point.
Causes close to her heart included helping homeless people, preventing suicide and supporting LGBT rights in the most restrictive regime in the UK.