| /dports/science/siesta/siesta-4.1.5/Util/TS/TBtrans/ |
| H A D | m_tbt_hs.F90 | 94 integer :: iHS, nspin local
135 iHS = 0
139 iHS = iHS + 1
193 tHS(iHS) = tmpHS(ipvt(iHS))
270 integer :: iHS local
297 do iHS = 1 , N_HS
300 call read_HS(ispin,tHS(iHS),files(iHS))
306 if ( iHS > 1 ) then
307 if ( .not. equivalent(files(iHS-1)%sp,files(iHS)%sp) ) then
313 if ( any(files(iHS-1)%lasto /= files(iHS)%lasto) ) then
[all …]
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| /dports/biology/vcflib/vcflib-1.0.2/doc/ |
| H A D | iHS.md | 1 % IHS(1) iHS (vcflib) | iHS (VCF statistics)
6 **iHS**
10 **iHS** --target 0,1,2,3,4,5,6,7 --file my.phased.vcf \ --region chr1:1-1000 > STDOUT 2> STDERR
14 **iHS** calculates the integrated haplotype score which measures the relative decay of extended hap…
23 …iHS** can be run without a genetic map, in which case the change in EHH is integrated over a const…
25 …iHS** analyses requires normalization by allele frequency. It is important that **iHS** is calcul…
29 …**iHS** calculates the integrated ratio of haplotype decay between the reference and non-reference…
36 6. **iHS** ln(iEHHalt/iEHHref)
84 [iHS.cpp](https://github.com/vcflib/vcflib/blob/master/src/iHS.cpp)
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| H A D | normalize-iHS.md | 1 % NORMALIZE-IHS(1) normalize-iHS (vcflib) | normalize-iHS (VCF genotype)
6 **normalize-iHS**
14 normalizes iHS or XP-EHH scores.
32 Output : **normalize-iHS** adds one additional column to input (normalized score).
33 required: -f -- Output from iHS or XPEHH
66 [normalize-iHS.cpp](https://github.com/vcflib/vcflib/blob/master/src/normalize-iHS.cpp)
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| H A D | segmentIhs.md | 10 segmentFst -s 2 -f iHS.normalized.output.txt
26 4. Average iHS
27 5. Average high Fst (iHS > -s)
28 6. N iHS values in segment
29 7. N high iHS values in segment
32 optional: -s -- High absolute iHS cutoff [2]
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| H A D | vcflib.md | 64 | [normalize-iHS](./normalize-iHS.md) | normalizes iHS or XP-EHH scores. |
146 …| [iHS](./iHS.md) | **iHS** calculates the integrated haplotype score which measures the relative …
|
| H A D | smoother.md | 37 wcFst, pFst, bFst, iHS, xpEHH, abba-baba, col3
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| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | normalize-iHS.cpp | 76 double iHS ; member
229 windat.push_back(data[i]->iHS); in normalize()
242 data[i]->niHS = (data[i]->iHS - avg) / (sd); in normalize()
279 tp->iHS = atof(lineDat[5].c_str()); in main()
313 << data[i]->iHS << "\t" in main()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | normalize-iHS.cpp | 67 double iHS ; member
209 windat.push_back(data[i]->iHS); in normalize()
222 data[i]->niHS = (data[i]->iHS - avg) / (sd); in normalize()
259 tp->iHS = atof(lineDat[5].c_str()); in main()
293 << data[i]->iHS << "\t" in main()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | normalize-iHS.cpp | 67 double iHS ; member
209 windat.push_back(data[i]->iHS); in normalize()
222 data[i]->niHS = (data[i]->iHS - avg) / (sd); in normalize()
259 tp->iHS = atof(lineDat[5].c_str()); in main()
293 << data[i]->iHS << "\t" in main()
|
| /dports/biology/vcflib/vcflib-1.0.2/paper/ |
| H A D | plos_latex_template.tex | 303 …iHS) measures the relative decay of \textit{EHH\textsubscript{c}} (Eq~[\ref{eq:EHHC}]) between the…
305 \begin{equation}\label{eq:iHS}
306 iHS = ln(\frac{\int \textrm{\textit{EHH}}_{c(alt)}}{ \int \textrm{EHH}_{c(ref)} } )
313 …ect within-population selection we applied the integrated haplotype score (iHS). These analyses s…
326 …iHS Manhattan plot for Norther Europeans (CEU). The x-axis is an index and the y-axis is the aver…
340 …iHS analyses we smoothed the data, counting the fraction of absolute iHS values above 2.5 in a 100…
342 …iHS score, see Fig. 2B. The HLA locus, \textit{NRG3}, \textit{KIAA0556} and \textit{ALG12} also s…
363 {\bf iHS analyses.} An archive of the snakemake file, the config file and region file used to run …
367 {\bf Comparison of iHS methods.} Scatter plots comparing VCFLIB's implementation of iHS to SELSCAN…
|
| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/paper/ |
| H A D | plos_latex_template.tex | 303 …iHS) measures the relative decay of \textit{EHH\textsubscript{c}} (Eq~[\ref{eq:EHHC}]) between the…
305 \begin{equation}\label{eq:iHS}
306 iHS = ln(\frac{\int \textrm{\textit{EHH}}_{c(alt)}}{ \int \textrm{EHH}_{c(ref)} } )
313 …ect within-population selection we applied the integrated haplotype score (iHS). These analyses s…
326 …iHS Manhattan plot for Norther Europeans (CEU). The x-axis is an index and the y-axis is the aver…
340 …iHS analyses we smoothed the data, counting the fraction of absolute iHS values above 2.5 in a 100…
342 …iHS score, see Fig. 2B. The HLA locus, \textit{NRG3}, \textit{KIAA0556} and \textit{ALG12} also s…
363 {\bf iHS analyses.} An archive of the snakemake file, the config file and region file used to run …
367 {\bf Comparison of iHS methods.} Scatter plots comparing VCFLIB's implementation of iHS to SELSCAN…
|
| H A D | plos_latex_template.aux | 37 \newlabel{eq:iHS}{{4}{3}{Haplotype methods (for phased variants)}{equation.0.4}{}}
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/paper/ |
| H A D | plos_latex_template.tex | 303 …iHS) measures the relative decay of \textit{EHH\textsubscript{c}} (Eq~[\ref{eq:EHHC}]) between the…
305 \begin{equation}\label{eq:iHS}
306 iHS = ln(\frac{\int \textrm{\textit{EHH}}_{c(alt)}}{ \int \textrm{EHH}_{c(ref)} } )
313 …ect within-population selection we applied the integrated haplotype score (iHS). These analyses s…
326 …iHS Manhattan plot for Norther Europeans (CEU). The x-axis is an index and the y-axis is the aver…
340 …iHS analyses we smoothed the data, counting the fraction of absolute iHS values above 2.5 in a 100…
342 …iHS score, see Fig. 2B. The HLA locus, \textit{NRG3}, \textit{KIAA0556} and \textit{ALG12} also s…
363 {\bf iHS analyses.} An archive of the snakemake file, the config file and region file used to run …
367 {\bf Comparison of iHS methods.} Scatter plots comparing VCFLIB's implementation of iHS to SELSCAN…
|
| H A D | plos_latex_template.aux | 37 \newlabel{eq:iHS}{{4}{3}{Haplotype methods (for phased variants)}{equation.0.4}{}}
|
| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/ |
| H A D | README.md | 876 ### iHS subsection
878 iHS calculates the integrated haplotype score which measures the relative decay of extended haploty…
880 iHS analyses requires normalization by allele frequency. It is important that iHS is calculated ov…
885 …iHS calculates the integrated ratio of haplotype decay between the reference and non-reference all…
892 6. iHS ln(iEHHalt/iEHHref)
897 iHS --target 0,1,2,3,4,5,6,7 --file my.phased.vcf \
935 wcFst, pFst, bFst, iHS, xpEHH, abba-baba
|
| /dports/biology/freebayes/freebayes-1.3.5/vcflib/ |
| H A D | README.md | 876 ### iHS subsection
878 iHS calculates the integrated haplotype score which measures the relative decay of extended haploty…
880 iHS analyses requires normalization by allele frequency. It is important that iHS is calculated ov…
885 …iHS calculates the integrated ratio of haplotype decay between the reference and non-reference all…
892 6. iHS ln(iEHHalt/iEHHref)
897 iHS --target 0,1,2,3,4,5,6,7 --file my.phased.vcf \
935 wcFst, pFst, bFst, iHS, xpEHH, abba-baba
|
| /dports/biology/vcflib/vcflib-1.0.2/ |
| H A D | README.md | 144 | [normalize-iHS](./doc/normalize-iHS.md) | normalizes iHS or XP-EHH scores. |
226 …| [iHS](./doc/iHS.md) | **iHS** calculates the integrated haplotype score which measures the relat…
|
| /dports/databases/pg_citus/citus-10.2.3/src/test/regress/data/ |
| H A D | customer.3.data | 51 1051|Customer#000001051|iHS,UFudVOOe|2|12-869-221-1428|9776.39|HOUSEHOLD|cuses boost furiously sile…
|
| /dports/biology/bbmap/bbmap/resources/ |
| H A D | blacklist_refseq_merged.sketch | 43004 5iHS?2H
|
| /dports/security/hashcat-legacy/hashcat-legacy-2.00/salts/ |
| H A D | brute-vbulletin.salt | 662677 iHS
|
| /dports/math/py-heyoka/heyoka.py-0.16.0/doc/notebooks/ |
| H A D | The Maxwell-Boltzmann distribution.ipynb | 452056 "Ep1DREREpFVcACMyII8fPxadoNdkWUZ8fLxax9y4dQ9yV+iHS/FNsXv/ERQtWlSt42eUnZ0dvsQr\\\n",
|