Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / GreenleafLab/NucleoATAC issues and pull requests

#97 - pyatac ins output returning all zero values

Issue - State: open - Opened by NatashaJansz about 3 years ago

#96 - Python 3 compatibility

Pull Request - State: open - Opened by AliciaSchep over 3 years ago - 1 comment

#95 - Port to Python 3 and pure python

Pull Request - State: closed - Opened by oaxiom over 3 years ago - 4 comments

#94 - nucleosome positioning question

Issue - State: open - Opened by juechenyang over 3 years ago

#93 - Errors

Issue - State: closed - Opened by juechenyang almost 4 years ago - 1 comment

#92 - Normalization and Differential peaks (Fig 5A, 5D)

Issue - State: open - Opened by monnieb92 almost 4 years ago - 1 comment

#91 - Question about the use of NucleoATAC.

Issue - State: open - Opened by chesterlee7246 about 4 years ago

#90 - Error in installation

Issue - State: open - Opened by pb016 about 4 years ago

#89 - maintainence and porting

Issue - State: open - Opened by shouldsee about 4 years ago

#88 - Interpreting NucleoATAC Output

Issue - State: open - Opened by StevenWingett almost 5 years ago

#86 - question about Supplementary Figure 18 in NucleoATAC paper

Issue - State: open - Opened by skye-12138 about 5 years ago

#85 - error with module nfr

Issue - State: closed - Opened by LuccaZhao over 5 years ago - 2 comments

#84 - occ

Issue - State: closed - Opened by Baharehh over 5 years ago - 1 comment

#83 - Understanding Nucleoatac outputs and Figure 7a from paper

Issue - State: open - Opened by Flope over 5 years ago - 1 comment

#82 - list index out of range

Issue - State: closed - Opened by michaelwillcockson almost 6 years ago - 1 comment

#81 - Broad vs narrow peaks for NucleoATAC

Issue - State: closed - Opened by mbaddoo almost 6 years ago - 4 comments

#80 - interpreting occupancy begraph file

Issue - State: closed - Opened by mbaddoo almost 6 years ago - 2 comments

#79 - Pygments versions 0.3.4

Issue - State: open - Opened by freshlearner about 6 years ago

#78 - Seperate Chromosome?

Issue - State: closed - Opened by hmyh1202 over 6 years ago - 5 comments

#77 - nucleoatac occ requires FASTA?

Issue - State: open - Opened by vreuter over 6 years ago - 1 comment

#76 - nucleoatac run

Issue - State: closed - Opened by hmyh1202 over 6 years ago - 1 comment

#75 - how to interpret V-plot

Issue - State: open - Opened by wanluliu over 6 years ago - 2 comments

#73 - Python3.x support?

Issue - State: closed - Opened by evanbiederstedt over 6 years ago - 5 comments

#72 - Narrow/Broad peaks for NucleoATAC

Issue - State: closed - Opened by jma1991 over 6 years ago - 2 comments

#71 - NucleoATAC ran out of memory

Issue - State: open - Opened by bliu100 over 6 years ago

#70 - `nucpos` files are empty

Issue - State: open - Opened by sameet over 6 years ago - 2 comments

#69 - biological interpretation of occupancy tracks

Issue - State: closed - Opened by bhatis2 over 6 years ago - 1 comment

#68 - Interpreting output

Issue - State: closed - Opened by pranithavangala over 6 years ago - 1 comment

#67 - nucleoatac not running

Issue - State: open - Opened by da-bar over 6 years ago

#66 - TypeError: 'int' object has no attribute '__getitem__'

Issue - State: closed - Opened by sudarshanchari almost 7 years ago - 8 comments

#65 - Tag for latest version (v3.4?)

Issue - State: closed - Opened by lparsons almost 7 years ago - 1 comment

#64 - fatal error: 'numpy/arrayobject.h' file not found

Issue - State: open - Opened by kesteph almost 7 years ago - 5 comments

#63 - are these results sensible?

Issue - State: open - Opened by avilella about 7 years ago - 3 comments

#62 - Incorrect Model Fit

Issue - State: open - Opened by mmilevskiy about 7 years ago - 5 comments

#61 - Figures 5B, C and D

Issue - State: closed - Opened by naiarabediaga about 7 years ago - 3 comments

#60 - NFR output of nucleoatac

Issue - State: closed - Opened by Flomass about 7 years ago - 4 comments

#59 - what's the bedtools slop -b size?

Issue - State: closed - Opened by crazyhottommy about 7 years ago - 2 comments

#58 - shifting reads bam for NucleoATAC?

Issue - State: closed - Opened by crazyhottommy about 7 years ago - 3 comments

#57 - RuntimeWarning: invalid value encountered in sqrt

Issue - State: open - Opened by ghost about 7 years ago - 1 comment

#56 - Can I run nucleoatac with a consensus peak file?

Issue - State: closed - Opened by ghost about 7 years ago - 2 comments

#55 - higher resolution nucpos.bed.gz is empty

Issue - State: open - Opened by igordot over 7 years ago - 30 comments

#54 - question about occ_track

Issue - State: closed - Opened by duyphamuab over 7 years ago - 2 comments

#53 - Error compiling Cython file

Issue - State: closed - Opened by IanCodes over 7 years ago - 5 comments

#52 - RuntimeWarning: overflow encountered in power

Issue - State: open - Opened by mfas7 over 7 years ago - 1 comment

#51 - Insertion sites plot around TSS

Issue - State: closed - Opened by krouskas over 7 years ago - 3 comments

#50 - Requirements

Issue - State: closed - Opened by saschi over 7 years ago - 1 comment

#49 - BAM file for fragment sizes distribution plot

Issue - State: closed - Opened by krouskas over 7 years ago - 1 comment

#48 - ValueError with NucleoATAC

Issue - State: closed - Opened by Scubatuba99 over 7 years ago - 2 comments

#47 - PWM descriptor file

Issue - State: closed - Opened by igordot almost 8 years ago - 1 comment

#46 - extending regions

Issue - State: closed - Opened by igordot almost 8 years ago - 1 comment

#45 - Profile plot using NucleoATAC around peak centers

Issue - State: closed - Opened by sudhirthakurela almost 8 years ago - 1 comment

#44 - Occupancy plot: observed and fitted occupancy differ

Issue - State: closed - Opened by ShaluJhanwar almost 8 years ago - 2 comments

#43 - Optimizing run time

Issue - State: closed - Opened by will-NYGC almost 8 years ago - 3 comments

#42 - Best way to normalize outputs for comparisons between conditions ?

Issue - State: closed - Opened by PFRoux almost 8 years ago - 1 comment

#41 - nucleoATAC applied to MNase

Issue - State: closed - Opened by uschwartz almost 8 years ago - 4 comments

#40 - Plots for Figure 4 E

Issue - State: closed - Opened by khayer almost 8 years ago - 1 comment

#39 - Insertions and coverage tracks

Issue - State: closed - Opened by DoaneAS about 8 years ago - 4 comments

#38 - nucleoatac .nucpos.bed problem

Issue - State: closed - Opened by danimschwartz about 8 years ago - 5 comments

#37 - RuntimeWarnings and ValueErrors

Issue - State: closed - Opened by msuperd1 about 8 years ago - 1 comment

#36 - Input bam and bed

Issue - State: closed - Opened by josegarciamanteiga about 8 years ago - 3 comments

#35 - Combining replicates

Issue - State: closed - Opened by PFRoux about 8 years ago - 4 comments

#34 - very slow nucleoatac run

Issue - State: closed - Opened by kenkclam over 8 years ago - 2 comments

#33 - error in nucleoatac run

Issue - State: closed - Opened by yanbianqu over 8 years ago - 2 comments

#32 - Step 1 Value Error

Issue - State: closed - Opened by harveyza over 8 years ago - 2 comments

#31 - Plots of paper Figure 1c

Issue - State: closed - Opened by antgomo over 8 years ago - 1 comment

#30 - ValueError: invalid reference

Issue - State: closed - Opened by OscarBrock over 8 years ago - 3 comments

#29 - NucleoATAC on a whole genome

Issue - State: closed - Opened by PFRoux over 8 years ago - 2 comments

#28 - PWM descriptor file for Mouse

Issue - State: closed - Opened by ahorvath over 8 years ago - 4 comments

#27 - Problems running example

Issue - State: closed - Opened by antgomo over 8 years ago - 1 comment

#26 - Mapped reads on Nucleosomes

Issue - State: closed - Opened by ShaluJhanwar over 8 years ago - 1 comment

#25 - IndexError: arrays used as indices must be of integer (or boolean) type

Issue - State: closed - Opened by ShaluJhanwar over 8 years ago - 7 comments

#24 - Regarding PWM Mouse Genome

Issue - State: closed - Opened by ShaluJhanwar over 8 years ago - 1 comment

#23 - Runtime Error

Issue - State: closed - Opened by OscarBrock over 8 years ago - 10 comments

#22 - Gamma

Pull Request - State: closed - Opened by AliciaSchep over 8 years ago

#21 - Overflow error

Issue - State: closed - Opened by OscarBrock over 8 years ago - 3 comments

#20 - nucleoATAC Invalid Region error

Issue - State: closed - Opened by OscarBrock over 8 years ago - 5 comments

#19 - test data set

Issue - State: closed - Opened by EricDeveaud over 8 years ago - 2 comments

#18 - How looks like a good NFR profile ?

Issue - State: closed - Opened by PFRoux over 8 years ago - 7 comments

#17 - Question about vprocess for mammalian data

Issue - State: closed - Opened by Angrydutchman over 8 years ago - 1 comment

#16 - Step 1 parameter optimization failure

Issue - State: closed - Opened by emilliman5 over 8 years ago - 7 comments

#15 - nucleoatac nfr problem

Issue - State: closed - Opened by will-NYGC over 8 years ago - 4 comments

#14 - --not_atac definition clarification?

Issue - State: closed - Opened by msg63 almost 9 years ago - 1 comment

#13 - Can't get nucleoatac to run

Issue - State: closed - Opened by Angrydutchman almost 9 years ago - 2 comments

#12 - Problem running NucleoAtac

Issue - State: closed - Opened by kesteph almost 9 years ago - 3 comments

#11 - chromsome discrepancy

Issue - State: closed - Opened by davek44 almost 9 years ago - 1 comment

#10 - pyatac pwm: OverflowError: can't convert negative value to unsigned int

Issue - State: closed - Opened by jebard almost 9 years ago - 2 comments

#9 - nucleoatac crashing after running partially

Issue - State: closed - Opened by laulabbrandeis almost 9 years ago - 3 comments

#8 - NucleoATAC installation

Issue - State: closed - Opened by srogue50 almost 9 years ago - 4 comments

#7 - question about output files

Issue - State: closed - Opened by duyphamuab almost 9 years ago - 4 comments

#6 - Relative paths are not handeled correctly

Issue - State: closed - Opened by balwierz about 9 years ago - 1 comment

#5 - Issue4

Pull Request - State: closed - Opened by AliciaSchep about 9 years ago

#4 - Problem building pyatac.fragments

Issue - State: closed - Opened by cdeboever3 about 9 years ago - 3 comments

#3 - Problem running

Issue - State: open - Opened by lopatica about 9 years ago - 6 comments

#2 - changed setup

Pull Request - State: closed - Opened by AliciaSchep over 9 years ago