Earlier quoted context omitted.
I don't want to dunk on you with really obvious suggestions like "you have a bad resume, fix it" type comments, maybe you've already had it looked over, and you're in a non-optimal location or something. Maybe ask a few specific questions on reddit somewhere like r/cscareerquestions.
I've been wracking my brain for years over this, and I'm still not any closer to understanding what the problem is. I've had my resume looked at and tweaked over and over. I never send a cover letter without having someone else proofread and offer suggestions. I've lived and worked in many tech-hub places, including San Francisco for 6 years. I just don't know... I think it's got to be socially related, but I have a…
There you have it. It's brutally unfair, but autism, if strong enough to be perceivable, sounds like the most likely cause: you're different, and people don't like you because of it.
Even worse, I believe that people on the autism spectrum don't even perceive they're different. I personally have no idea whether I'm on that spectrum, or how far. Still: my own Mom once stated the "obvious": that I must notice that I'm not like others. I had to tell her that I don't. At 35.
So. People perceive you're different. It's obvious enough that they expect you to perceive that difference, even though you may not. So when you fail to conform to the obscure (to you) group norm, they end up rejecting you. Perhaps even rationalising that you're doing it on purpose (remember, the difference is obvious to them). Then you're out of the group.
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There may be other factors as well. Folks tend to be kinder, more forgiving, of pretty people, so if you can improve that in any way, try to do so (one habit at a time though, take it easy). The easiest thing to go for, I think, is clothing: try having someone you trust chose your clothes for you. Pay explicit attention to the dress code at your workplace, emulate it a little (but don't buy the exact same clothes either!). Also consider light makeup if you're a woman (and maybe get counsel about that too).
Much harder is taking good care of your health. If you're fat, unfit, or otherwise unhealthy, try to work on that. Sleeping well, eating well, and exercising properly is surprisingly hard when you're not used to it, but it's a must.
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Edit: also consider telling your colleagues about your autism. I expect it's not easy, and it may not even be a good idea, but there's a chance that people knew why you are the way you are, they'd tolerate it better.