Neurosurgery-Brain-Tumor-Center-DiazLab/CONICS

Issues

• Can not find SUVA_CNVs_BIC_LR.txt

  #46 opened 4 months ago by jianyangdu
  0

• Error in hclust(d, method = method) : size cannot exceed 65536

  #45 opened 5 months ago by wwYinYin
  0

• Error in plotAll

  #41 opened 2 years ago by marie2T
  2

• Issue Running CONICSMat Tutorial Due To Deprecated SCRAN Function

  #25 opened 4 years ago by MayaTalukdar
  6

• CONICS Sample Data Availability

  #44 opened a year ago by elisafazz
  0

• error in classify tumor cell and nontumor cell?

  #12 opened 5 years ago by zhumengyan
  6

• chromosome arm positions of mouse?

  #38 opened 3 years ago by Li-ZhiD
  1

• Segmentation fault

  #43 opened a year ago by archana433
  0

• getGenePositions parameter got the wrong location information

  #36 opened 3 years ago by sunshine1126
  3

• Error in getGenePositions

  #40 opened 2 years ago by TM9013
  1

• Few tumor cell

  #39 opened 2 years ago by sunshine1126
  0

• detection of CNV in germlines

  #37 opened 3 years ago by lmanchon
  1

• CONICSmat install failed

  #35 opened 3 years ago by Sumithrasank
  0

• error on plotall

  #28 opened 4 years ago by FuqianShi
  1

• Can CONICS be used with 3'- tag sequencing methods ?

  #34 opened 4 years ago by moutazhelal
  1

• Where can I get the chromosome arm positions file for mouse?

  #33 opened 4 years ago by smk5g5
  0

• Conicsmat throws an error for filterMatrix()

  #32 opened 4 years ago by biobug16
  0

• Issue about CONICSmat in getGenePositions function

  #31 opened 4 years ago by GalaxyYang
  0

• CONICS for scATAC-seq

  #30 opened 4 years ago by camiel-m
  0

• unable to install CONICSmat

  #29 opened 4 years ago by liron27
  0

• error on plotall

  #27 opened 4 years ago by FuqianShi
  0

• How to check amplification of a specific gene using CONICSmat?

  #26 opened 4 years ago by biobug16
  2

• How can we use RPKM or TPM values for prediction of CNVs or tumour cells?

  #24 opened 5 years ago by avln24
  0

• How can we set a seed to reproduce the same figure with plotHistogram() in CONICSmat?

  #22 opened 5 years ago by biobug16
  0

• Can we select cells with a specific CNV?

  #21 opened 5 years ago by biobug16
  0

• Can or should we do batch-correction before parsing the log2cpm to CONICSmat?

  #20 opened 5 years ago by biobug16
  0

• Questions about predicted cell types as an optional input for CONICSmat and optimizing number of clusters for heatmap

  #19 opened 5 years ago by avln24
  0

• How can we use tpm values provided in GEO datasets for CNV or tumor cell prediction

  #18 opened 5 years ago by biobug16
  2

• Questions about the input expression matrix and threshold used in plotChromosomeHeatmap

  #13 opened 5 years ago by YiweiNiu
  3

• Heatmap of the posterior probabilities highlights cells in red (down-regulation of 1p/19q) and not in blue (up-regulation)

  #17 opened 5 years ago by biobug16
  2

• getGenePositions() in CONICSmat can not deal with gene names in ENSEMBL format

  #15 opened 5 years ago by biobug16
  1

• How to process the natural log values from Seurat into log2(CPM/10+1)

  #16 opened 5 years ago by biobug16
  3

• Error in string.to.colors() in Tutorial

  #9 opened 5 years ago by erin-d
  3

• chromosome arm positions hg19

  #11 opened 5 years ago by ccruizm
  1

• fail to install CONISmat

  #14 opened 5 years ago by RitataLU
  1

• if the package can be applied to 10X scRNA-Seq data

  #6 opened 5 years ago by zhumengyan
  2

• Error in tutorial

  #8 opened 5 years ago by romagnolid
  5

• Heatmap visualization and chromosome position file

  #4 opened 6 years ago by gufranca
  12

• error on "plotChromosomeHeatmap" function within 10x scRNA data

  #7 opened 6 years ago by helianthuszhu
  1

• Confusion about the calcNormFactors

  #3 opened 6 years ago by ysbioinfo
  9

• error when connecting to BioMart

  #2 opened 7 years ago by ysbioinfo
  5

• extract the samples with CNV

  #1 opened 7 years ago by QSong-github
  5