![]() In this manner, maser can quickly identify splicing affecting known protein domains, extracellular and transmembrane regions, as well as mutation sites in the protein. Visualization of transcripts and protein affected by splicing using custom Gviz plots.Ī key feature of the package is mapping of splicing events to protein features such as topological domains, motifs and mutation sites provided by the UniprotKB database and visualized along side the genomic location of splicing.Integration with UniprotKB for batch annotation of protein features overlapping splicing events.Mapping of splicing events to Ensembl transcripts and UniprotKB proteins.Analysis of global splicing effects using boxplots, principal component analysis and volcano plots.Filtering of rMATS splicing events based on RNA-seq coverage, p-values and differential percent spliced-in (PSI).Overall, maser allows a detailed analysis of splicing events identified by rMATS by implementing the following functionalities: We developed maser ( Mapping Alternative Splicing Events to p Roteins) package to enable functional characterization of splicing in both transcriptomic and proteomic contexts. However, functional interpretation of splicing requires the integration of heterogeneous data sources such as transcriptomic and proteomic information. Thread overview: 5+ messages (download: mbox.Alternative splicing occurs in most human genes and novel splice isoforms may be associated to disease or tissue specific functions. I don't have a hard feelingĮnd of thread, other threads: It keeps it closer to the tss.len test, so I'd leave it for that reason,īut on the other hand the compiler should be perfectly able to optimise it ![]() Perhaps avoiding unneeded delta could be worthy. The only minor thing that I note is that the above > Even when tcp_splice_read() reads all it was asked for, for blocking > On Fri, at 14:33 +0100, Pavel Begunkov wrote: To: Paolo Abeni, netdev, edumazet, davem, dsahern, kuba 13:52 ` Paolo Abeni 12:51 ` Pavel Begunkov 0 siblings, 0 replies 5+ messages in threadįrom: Pavel Begunkov 12:51 UTC ( / raw) * Re: net/tcp: optimise locking for blocking splice The only minor thing that I note is that the aboveĬhunk is not needed. > timeo = sock_rcvtimeo(sk, sock->file->f_flags & O_NONBLOCK) > diff -git a/net/ipv4/tcp.c b/net/ipv4/tcp.c > 1 file changed, 5 insertions(+), 3 deletions(-) ![]() > That saves us one release_sock() lock_sock() pair per successful > Check tss.len right after we adjust it, and return if we're done. > sockets it'll release and immediately regrab the socket lock, loop if (ret Even when tcp_splice_read() reads all it was asked for, for blocking Timeo = sock_rcvtimeo(sk, sock->file->f_flags & O_NONBLOCK) ġ file changed, 3 insertions(+), 3 deletions(-) That saves us one release_sock() lock_sock() pair per successfulġ file changed, 5 insertions(+), 3 deletions(-)ĭiff -git a/net/ipv4/tcp.c b/net/ipv4/tcp.c Sockets it'll release and immediately regrab the socket lock, loopĬheck tss.len right after we adjust it, and return if we're done. 13:33 TCP splice improvements Pavel 13:33 ` Pavel Begunkovġ sibling, 1 reply 5+ messages in threadĮven when tcp_splice_read() reads all it was asked for, for blocking * net/tcp: optimise locking for blocking splice Net/tcp: optimise locking for blocking spliceġ file changed, 8 insertions(+), 6 deletions(-) The main part is in Patch 1, which optimises locking for successfulīlocking TCP splice read, following with a clean up in Patch 2. ![]() To: netdev, edumazet, davem, dsahern, pabeni, kuba +Cc: Pavel Begunkov 13:33 ` net/tcp: optimise non error splice paths Pavel BegunkovĠ siblings, 2 replies 5+ messages in threadįrom: Pavel Begunkov 13:33 UTC ( / raw) 13:33 ` net/tcp: optimise locking for blocking splice Pavel Begunkov TCP splice improvements archive mirror help / color / mirror / Atom feed * TCP splice improvements 13:33 Pavel Begunkov
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