Yellow crime scene tape that seems to stretch across American is still in place at the school, following the deadly school shooting that killed a fellow student and teacher, and injured five others.
The suspect, Natalie Rupnow, who went by Samantha, died from a self-inflicted gunshot wound, police said.
"I don't know whether [the shooter] was transgender or not," Barnes said at a news conference on Monday night, when asked about Rupnow's gender identity.
"I don't think that whatever happened today has anything to do with how she or he or they may have wanted to identify," he said. "And I wish people would kind of leave their own personal biases out of this."
The motive appears to be a combination of factors, Madison Police Chief Shon Barnes said at a news conference Tuesday.
Police are talking to students to determine if bullying was one of the factors, he said.
"Everyone was targeted in this incident and everyone was put in equal danger," Barnes said.
On the Facebook page of the shooter's father, a banner photo shows a young girl skeet shooting with a long gun. And according to comments on the page, it is believed that person is Abundant Life school shooter.
While she is seen with a long gun at a shooting club near Madison in the August Facebook photo, it was a 9mm pistol that police say she used in the rampage on her new school.
That photo and other numerous social media posts and pictures are among the possible red flags under investigation by police and federal law enforcement.
"There are always signs of a school shooting before it occurred," Madison Police Chief Shon Barnes said at a Tuesday news conference. "Some of you have reached out about Rupnow's social media activity prior to yesterday shooting. We're looking into her online activity."
In the minutes before the shooting, multiple social media posts from an account believed to belong to the shooter show a person in a bathroom stall, making a hand gesture that has been used by white supremacist mass shooters.
Another post from that same account prior to the shooting included a link to a Google Drive account. Police are still investigating whether that drive contained a six-page declaration that has circulated on the internet with the shooter's name on it.
If this Google drive linking to the pronouncement does turn out to be her suicide note, the declaration lays out numerous possible personal motives and attempted explanations for the authorities to investigate.
Investigators are also focusing on clues from the home where the 15-year-old shooter lived with her father. The front door to the home was ripped off by police evidence teams serving a search warrant Monday night.
Investigators say they also want an inventory of all guns the shooter had access to.
The teen shooter used a handgun, police said. Authorities are investigating the origin of the firearm, according to Barnes.
They are also speaking with her father and "trying to determine what he knew or may have not known about what happened today," Barnes said.
"But again, he lost someone as well," Barnes added.
Police believe that the suspect was in school when the attack began, and that there wasn't any breach.
Local police have now turned over the teen's electronic equipment to FBI evidence technicians, looking for a motive and whether friends or family members had knowledge that there was an attack plot or had been warned that violence was to happen yesterday.
"If they missed a red flag and chose not to address it, if she made overt actions and overt statements that she wants to kill and they didn't do it, that should be considered too," said Daniel Brunner, a retired FBI supervisory special agent.
The Facebook picture of the shooter at a Wisconsin gun range shows her wearing a black t-shirt that has the logo of a German band which was a favorite of one of the Columbine High School killers, who murdered 13 people.
Whether she was motivated by the Columbine killers or just had an affinity for them, police are hoping to determine.
ABC News contributed to this report.