NCI-CCDI CCDITEGS_Bioinformatics issues

NCI-CCDI / CCDITEGS_Bioinformatics

This is an internal repository to track tasks on Project boards as issues

0 stars 0 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

TEGS4_Run second phase of analysis - Pie chart

#95 Krithika-Bhuvan opened 4 months ago
0
TEGS4_Run second phase of analysis - Volcano plot

#94 Krithika-Bhuvan opened 4 months ago
0
TEGS3_Predict TF binding site in DLK1 super enhancer region using homer and add to IGV view

#93 wuy24 opened 4 months ago
0
CCDI6_Run Ying snmulti ome pipeline on the dataset

#92 Krithika-Bhuvan opened 4 months ago
0
TEGS3_Check how PRC2 complex components (SUZ12 and EED) will affect DLK1 expression in different cancer cell lines

#91 wuy24 opened 4 months ago
0
CCDI5_Look into Doublet challenges for this dataset

#90 Krithika-Bhuvan opened 4 months ago
0
CCDI5_Summarize stats from cell ranger on the GEX and ATAC data

#89 Krithika-Bhuvan opened 4 months ago
0
CCDI5_Create cleaned clinical file as input

#88 Krithika-Bhuvan opened 4 months ago
0
TEGS9_Run juicer on one sample of the real dataset

#87 Krithika-Bhuvan opened 4 months ago
0
TEGS2_Generate marker genes for each clusters and share with Carol's Team

#86 wuy24 opened 4 months ago
0
TEGS9_ Run Initial QC (Fastqc, trimming, Post-trim fastqc, Multi QC)

#85 Krithika-Bhuvan opened 4 months ago
0
TEGS4_Run second phase of analysis - Custom GSEA

#84 Krithika-Bhuvan opened 4 months ago
0
TEGS12_Get in touch with Samarth Mathur and Vineela Gangalapudi regarding how to use hg19 as reference in Xavier

#83 wuy24 opened 4 months ago
0
TEGS4_Run Tobias on ATACseq data

#82 Krithika-Bhuvan opened 4 months ago
0
TEGS12_Check output file from Xavier pipeline ran by Taylor

#81 wuy24 opened 4 months ago
0
TEGS3_Load data from NB and MPNST cells line from Zhihui and Xiyuan to IGV and share data with Jack and George

#80 wuy24 opened 4 months ago
0
TEGS2_Run the pipeline for the second ChemoTreatment samples and Perform analysis

#79 wuy24 opened 4 months ago
0
TEGS2_Run the pipeline for first ChemoTreatment samples and Perform analysis

#78 wuy24 opened 4 months ago
0
TEGS2_Run the pipeline for invitro samples and Perform analysis

#77 wuy24 opened 4 months ago
0
TEGS2_Build pipeline for Analyzing SPLINTR barcoded scRNASeq data from PDX samples

#76 wuy24 opened 4 months ago
0
CCDI4_Check what the cells removed by ATAC criteria are

#75 wuy24 opened 4 months ago
0
CCDI4_Generate snMultiome workflow using LucidChart

#74 wuy24 opened 4 months ago
0
CCDI4_Test ATAC CNV software RIDDLER

#73 wuy24 opened 4 months ago
0
CCDI4_Test GEX CNV software infercnv and scevan

#72 wuy24 opened 4 months ago
0
TEGS9_Use juicebox for secondary analysis

#71 Krithika-Bhuvan opened 5 months ago
0
TEGS9_Run Juicer on the trimmed data

#70 Krithika-Bhuvan opened 5 months ago
0
TEGS9_Merge technical replicates

#69 Krithika-Bhuvan opened 5 months ago
0
TEGS9_Read about HiC and see which pipeline is the right one

#68 Krithika-Bhuvan opened 5 months ago
0
TEGS1_Make a clean script for heatmap plot to share with Sophia

#67 wuy24 opened 5 months ago
0
TEGS2_Figure out how to handle human and mouse cells from PDX samples

#66 wuy24 opened 5 months ago
0
CCDI4_Work on ATAC portion of Multiome data QC, clustering and integration.

#65 wuy24 opened 5 months ago
0
TEGS5_Script for ORA and GSEA analysis

#64 wuy24 opened 5 months ago
0
CCDI5_Connect with Neeraja regarding dataset and sample quality

#63 Krithika-Bhuvan opened 5 months ago
0
TEGS8_Run GSEA in R

#62 Krithika-Bhuvan opened 5 months ago
0
CCDI6_Cell line vs Xenograft PDX multiome comparison

#61 Krithika-Bhuvan opened 5 months ago
0
CCDI5_Run GEX on Troy's data

#60 Krithika-Bhuvan opened 5 months ago
0
TEGS9_Run juicer on test data

#59 Krithika-Bhuvan opened 5 months ago
0
CCDI2_Update workflow diagram

#58 Krithika-Bhuvan opened 5 months ago
0
CCDI2_Move files to s3 bucket, create meta data files

#57 Krithika-Bhuvan opened 5 months ago
1
TEGS4_Run secondary analysis on ATAC-seq data

#56 Krithika-Bhuvan opened 5 months ago
0
TEGS1_Run IPA comparison analysis on control vs treatment comparison for each cell line

#55 Krithika-Bhuvan opened 5 months ago
0
TEGS1_Run IPA core analysis on control vs treatment comparison for each cell line

#54 Krithika-Bhuvan opened 5 months ago
0
TEGS5_iDEP secondary analysis

#53 wuy24 opened 5 months ago
0
CCDI4_work on script for ATAC part of the Multiome data analysis

#52 wuy24 opened 5 months ago
0
TEGS11_Get IGV visualization for DLK1, MEG3, CDK8 from the GEO collection

#51 wuy24 opened 5 months ago
0
TEGS11_Pull down data from GEO collection(RNASeq,ChIPSeq,Methalation)

#50 wuy24 opened 5 months ago
0
TEGS2_Test SINCLAIR pipeline for GEX data integration

#49 wuy24 opened 5 months ago
0
CCDI4_test SINCLAIR for GEX data integration

#48 wuy24 opened 5 months ago
0
TEGS1_Baseline comparison group by MYCN and NAPRT staus

#47 wuy24 opened 5 months ago
0
TEGS5_Re-analysis of RNA-Seq data using new reference by adding CART to the genome using SF pipeline

#46 wuy24 opened 6 months ago
0