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NCI-CCDI
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CCDITEGS_Bioinformatics
This is an internal repository to track tasks on Project boards as issues
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TEGS4_Run second phase of analysis - Pie chart
#95
Krithika-Bhuvan
opened
9 months ago
0
TEGS4_Run second phase of analysis - Volcano plot
#94
Krithika-Bhuvan
opened
9 months ago
0
TEGS3_Predict TF binding site in DLK1 super enhancer region using homer and add to IGV view
#93
wuy24
opened
9 months ago
0
CCDI6_Run Ying snmulti ome pipeline on the dataset
#92
Krithika-Bhuvan
opened
9 months ago
0
TEGS3_Check how PRC2 complex components (SUZ12 and EED) will affect DLK1 expression in different cancer cell lines
#91
wuy24
opened
9 months ago
0
CCDI5_Look into Doublet challenges for this dataset
#90
Krithika-Bhuvan
opened
9 months ago
0
CCDI5_Summarize stats from cell ranger on the GEX and ATAC data
#89
Krithika-Bhuvan
opened
9 months ago
0
CCDI5_Create cleaned clinical file as input
#88
Krithika-Bhuvan
opened
9 months ago
0
TEGS9_Run juicer on one sample of the real dataset
#87
Krithika-Bhuvan
opened
9 months ago
0
TEGS2_Generate marker genes for each clusters and share with Carol's Team
#86
wuy24
opened
9 months ago
0
TEGS9_ Run Initial QC (Fastqc, trimming, Post-trim fastqc, Multi QC)
#85
Krithika-Bhuvan
opened
9 months ago
0
TEGS4_Run second phase of analysis - Custom GSEA
#84
Krithika-Bhuvan
opened
9 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
9 months ago
0
TEGS4_Run Tobias on ATACseq data
#82
Krithika-Bhuvan
opened
9 months ago
0
TEGS12_Check output file from Xavier pipeline ran by Taylor
#81
wuy24
opened
9 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
9 months ago
0
TEGS2_Run the pipeline for the second ChemoTreatment samples and Perform analysis
#79
wuy24
opened
9 months ago
0
TEGS2_Run the pipeline for first ChemoTreatment samples and Perform analysis
#78
wuy24
opened
9 months ago
0
TEGS2_Run the pipeline for invitro samples and Perform analysis
#77
wuy24
opened
9 months ago
0
TEGS2_Build pipeline for Analyzing SPLINTR barcoded scRNASeq data from PDX samples
#76
wuy24
opened
9 months ago
0
CCDI4_Check what the cells removed by ATAC criteria are
#75
wuy24
opened
9 months ago
0
CCDI4_Generate snMultiome workflow using LucidChart
#74
wuy24
opened
9 months ago
0
CCDI4_Test ATAC CNV software RIDDLER
#73
wuy24
opened
9 months ago
0
CCDI4_Test GEX CNV software infercnv and scevan
#72
wuy24
opened
9 months ago
0
TEGS9_Use juicebox for secondary analysis
#71
Krithika-Bhuvan
opened
10 months ago
0
TEGS9_Run Juicer on the trimmed data
#70
Krithika-Bhuvan
opened
10 months ago
0
TEGS9_Merge technical replicates
#69
Krithika-Bhuvan
opened
10 months ago
0
TEGS9_Read about HiC and see which pipeline is the right one
#68
Krithika-Bhuvan
opened
10 months ago
0
TEGS1_Make a clean script for heatmap plot to share with Sophia
#67
wuy24
opened
10 months ago
0
TEGS2_Figure out how to handle human and mouse cells from PDX samples
#66
wuy24
opened
10 months ago
0
CCDI4_Work on ATAC portion of Multiome data QC, clustering and integration.
#65
wuy24
opened
10 months ago
0
TEGS5_Script for ORA and GSEA analysis
#64
wuy24
opened
10 months ago
0
CCDI5_Connect with Neeraja regarding dataset and sample quality
#63
Krithika-Bhuvan
opened
10 months ago
0
TEGS8_Run GSEA in R
#62
Krithika-Bhuvan
opened
10 months ago
0
CCDI6_Cell line vs Xenograft PDX multiome comparison
#61
Krithika-Bhuvan
opened
10 months ago
0
CCDI5_Run GEX on Troy's data
#60
Krithika-Bhuvan
opened
10 months ago
0
TEGS9_Run juicer on test data
#59
Krithika-Bhuvan
opened
10 months ago
0
CCDI2_Update workflow diagram
#58
Krithika-Bhuvan
opened
10 months ago
0
CCDI2_Move files to s3 bucket, create meta data files
#57
Krithika-Bhuvan
opened
10 months ago
1
TEGS4_Run secondary analysis on ATAC-seq data
#56
Krithika-Bhuvan
opened
10 months ago
0
TEGS1_Run IPA comparison analysis on control vs treatment comparison for each cell line
#55
Krithika-Bhuvan
opened
10 months ago
0
TEGS1_Run IPA core analysis on control vs treatment comparison for each cell line
#54
Krithika-Bhuvan
opened
10 months ago
0
TEGS5_iDEP secondary analysis
#53
wuy24
opened
10 months ago
0
CCDI4_work on script for ATAC part of the Multiome data analysis
#52
wuy24
opened
10 months ago
0
TEGS11_Get IGV visualization for DLK1, MEG3, CDK8 from the GEO collection
#51
wuy24
opened
10 months ago
0
TEGS11_Pull down data from GEO collection(RNASeq,ChIPSeq,Methalation)
#50
wuy24
opened
10 months ago
0
TEGS2_Test SINCLAIR pipeline for GEX data integration
#49
wuy24
opened
10 months ago
0
CCDI4_test SINCLAIR for GEX data integration
#48
wuy24
opened
10 months ago
0
TEGS1_Baseline comparison group by MYCN and NAPRT staus
#47
wuy24
opened
10 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
11 months ago
0
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