misc

misc copied to clipboard

. |-- README # README |-- biodb # interface to biological databases | -- batchUCSC.pl # batch UCSC data retrieval; http://lh3lh3.users.sourceforge.net/ucsc-mysql.shtml |-- klib.lua # the klib Lua library (from http://bit.ly/klibgit) |-- math # mathematics | |-- matmul_SSE # matrix multiplication in a few languages; plus SSE example | | |-- matmul-double.c # double numbers | | |-- matmul.c # float numbers; plus SSE implementation | | |-- matmul.js # javascript implementation | | |-- matmul.lua # lua implementation | | -- matmul.pl # perl implementation | |-- lsoda.c # LSODA ODE solver | -- unequal-jk.c # block Jackknife; requiring klib/ksort.h |-- popgen # population genetics | -- genetic_dist.js # compute the genetic distance from deCODE genetic maps |-- seq # sequence analysis | |-- seqbility # unitilities to compute mappability http://bit.ly/snpable | | |-- apply_mask_l.c # apply a mask to a list of sites | | |-- apply_mask_s.c # apply a mask to a sequence | | |-- gen_mask.c # generate a mask from a raw mask | | |-- gen_raw_mask.pl # generate a raw mask from BWA SAM output | | |-- splitfa.c # split a reference sequence to overlapping short mers | | |-- uniq-dist-acc.pl # get the accumulative distribution from uniq-dist output | | |-- uniq-dist-cmp.pl # compare to uniq-dist output | | |-- uniq-dist.c # compute the distance between adjacent loci in unique regions | | -- [...] | |-- seqtk # toolkit for manipulation FASTA/Q files | | -- [...] | |-- bc2rg.lua # generate the RG SAM tag from the BC tag | |-- bioutils.lua # collection of bioinfo related (tiny) utilites | -- sam2bp.lua # collect break points from a SAM file containing split hits -- sys # system related programs `-- asub # array job submiter