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407 results • Page
1 of 9
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Views
Votes
Replies
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 2 hours ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
70
votes
29
replies
14k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 5 days ago by
jkbonfield
★ 1.2k • written 5.0 years ago by
finswimmer
16k
46
votes
13
replies
14k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 7 days ago by
Konstantinos
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.1k
2
votes
0
replies
144
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
22 days ago by
Novogene
▴ 410
3
votes
0
replies
161
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
22 days ago by
Novogene
▴ 410
3
votes
0
replies
354
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 6 weeks ago by
zx8754
11k • written 6 weeks ago by
Ming Tommy Tang
★ 3.8k
0
votes
0
replies
257
views
Tutorial:
How to convert sra files to fastq files using parallelized fastq-dump
fastq
sra
8 weeks ago by
Ming Tommy Tang
★ 3.8k
1
vote
5
replies
464
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 8 weeks ago by
Ram
43k • written 8 weeks ago by
Julia Ma
▴ 120
3
votes
2
replies
414
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 8 weeks ago by
ATpoint
81k • written 9 weeks ago by
Julia Ma
▴ 120
2
votes
1
reply
299
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq
space
clustering
updated 9 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
0
votes
1
reply
228
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq
MetaTiME
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
0
votes
0
replies
191
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq
SCSA
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
0
votes
0
replies
184
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq
SCSA
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
1
vote
0
replies
201
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq
SCSA
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
0
votes
0
replies
210
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
1
vote
0
replies
243
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
0
votes
0
replies
175
views
Tutorial:
How to Label the Y Axis with percentage sign and Order Bars in ggplot2 using a single cell dataset
seurat
single-cell
ggplot2
9 weeks ago by
Ming Tommy Tang
★ 3.8k
1
vote
0
replies
224
views
Tutorial:
How to Use Biomart to Find Mouse Orthologs for Human Genes
ids
gene
bioconductor
9 weeks ago by
Ming Tommy Tang
★ 3.8k
0
votes
0
replies
232
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
0
votes
1
reply
439
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
2
votes
0
replies
304
views
Tutorial:
Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA
RNA-seq
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
1
vote
0
replies
191
views
Tutorial:
Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
1
vote
1
reply
243
views
Tutorial:
Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING
ppi
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
2
votes
3
replies
424
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis with DEseq2
python
pyDESeq2
RNA-seq
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
6
votes
1
reply
348
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
0
votes
0
replies
185
views
Tutorial:
Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python
RNA-seq
batch-correction
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Julia Ma
▴ 120
49
votes
28
replies
11k
views
12 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
10 weeks ago by
Ram
43k
39
votes
16
replies
35k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 11 weeks ago by
GenoMax
140k • written 3.6 years ago by
lavinia.gordon
▴ 160
1
vote
0
replies
300
views
Tutorial:
4 CITE-seq tutorials
CTIE-seq
12 weeks ago by
Ming Tommy Tang
★ 3.8k
3
votes
3
replies
1.1k
views
Tutorial:
multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation
RNAseq
multiomics
updated 10 weeks ago by
sil_bioinfo
▴ 40 • written 6 months ago by
Ming Tommy Tang
★ 3.8k
16
votes
3
replies
4.2k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
cancer
methylation
RNA-Seq
R
updated 3.0 years ago by
zhuanggj706
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.1k
0
votes
0
replies
305
views
Tutorial:
download metadata using GEOquery
computational-biology
GEO
metadata
updated 3 months ago by
Ram
43k • written 3 months ago by
Ming Tommy Tang
★ 3.8k
1
vote
0
replies
276
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
3 months ago by
Ming Tommy Tang
★ 3.8k
0
votes
0
replies
327
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
3 months ago by
rohitsatyam102
▴ 840
0
votes
0
replies
420
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
4 months ago by
rohitsatyam102
▴ 840
0
votes
4
replies
636
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
4 months ago by
Coremine Medical
▴ 20
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 4 months ago by
Ram
43k • written 10.4 years ago by
Irsan
★ 7.8k
1
vote
0
replies
465
views
Tutorial:
How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq
heatmap
rstats
TCGA
4 months ago by
Ming Tommy Tang
★ 3.8k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 4 months ago by
ha2606
• 0 • written 6.2 years ago by
vimalkvn
▴ 320
2
votes
0
replies
532
views
Tutorial:
Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf
sparql
data-management
graph
updated 6 months ago by
Ram
43k • written 6 months ago by
Pierre Lindenbaum
160k
0
votes
1
reply
486
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 6 months ago by
ATpoint
81k • written 6 months ago by
JC
▴ 30
4
votes
2
replies
2.7k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 6 months ago by
GenoMax
140k • written 3.9 years ago by
ATpoint
81k
0
votes
0
replies
624
views
Tutorial:
T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq
TCR
single-cell
computational
biology
7 months ago by
Ming Tommy Tang
★ 3.8k
14
votes
3
replies
19k
views
Tutorial:
Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome
plot
coverage
samtools
updated 7 months ago by
William
▴ 30 • written 7.0 years ago by
kirannbishwa01
★ 1.6k
6
votes
2
replies
1.0k
views
Tutorial:
Updated List of Unix tutorials 2023
Unix
updated 7 months ago by
Ram
43k • written 7 months ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
482
views
Tutorial:
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome
rstats
spatial
single-cell
7 months ago by
Ming Tommy Tang
★ 3.8k
9
votes
4
replies
5.2k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
7 months ago by
Hamid Ghaedi
3.1k
6
votes
0
replies
553
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
7 months ago by
barslmn
★ 2.1k
1
vote
0
replies
602
views
Tutorial:
common mistakes in using spreadsheets
excel
spreadsheet
structured-data
updated 7 months ago by
Ram
43k • written 7 months ago by
Ming Tommy Tang
★ 3.8k
3
votes
1
reply
597
views
Tutorial:
Coordinate Systems and genomic variant description
coordinate-system
HGVS
normalization
VCF
updated 7 months ago by
Ram
43k • written 7 months ago by
Juke34
8.5k
407 results • Page
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Recent Votes
Comment: Average expression of a sample in single-cell data
A: Normalize FPKM values for cross-sample comparisons?
Answer: ColabFold
C: How To Convert Arabidopsis Gene Id To Ncbi Geneid, Ncbi-Gi Or Uniprot?
Troubleshooting a REGENIE sex-stratified GWAS
ENVO Ontology to Annotate Plain Text
Answer: Seurat 5 integration
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Answer: Deeptools scale issue for plotHeatmap
by
Learner
• 0
Hi Devon, Thanks a lot for the reply. DNA methylation file has 19466838 lines while domains has 92409 lines.
Answer: why there is an asterisk symbol at the end of each proteins sequences offasta fi
by
Juke34
8.5k
It corresponds to stop codon but in theory GTF format does not have stop codon in CDS. Keep in mind that it exists stop codon reading th…
Comment: scRNAseq normalization
by
ATpoint
81k
That is an entirely different analysis and depends on the testing Framework. If you use the commonly-used Wilcox test or something like lim…
Answer: Haddock 2.4
by
Preeti
• 0
i have three different runs with haddock score of -75, -68, -61 . Which one is better among these( molecule 1 is same in all three ,only mo…
Comment: NGS/GATK pipeline returns too many variants
by
dhruti
• 0
@dodausp Did you ever find a reason for this? I am having the same problem
Comment: Troubleshooting a REGENIE sex-stratified GWAS
by
Corentin
▴ 600
Sex chromosomes are always a bit tricky to handle in associations studies. How many male cases and male controls you have for this phenoty…
Answer: Haddock 2.4
by
Preeti
• 0
I want to know that which results from haddock are good like I got highest haddock score of -75 .....is it a good haddock score or not
Comment: Beagle Phasing and Imputation
by
Duarte Molha
▴ 240
Hi @lchart Thank you for your answer. I coded my male sample as biallelelic homozygous as i was aware of limitations for allosomes.…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
And I also change the chrom name in the .sizes file. That works perfect. Thank you very much!
Comment: scRNAseq normalization
by
sarahmanderni
▴ 100
Thanks for the response! I also was wondering to ask if you have found the log-norm also working fine in terms of downstream analysis like …
Answer: Subsetting Seurat object based on list of cell barcodes
by
fracarb8
★ 1.5k
`subset(seurat.obj_combined, cells = all_good_cells_rhemac10$V1)` You need to pass `cells` not `subset`. From the documentation: sub…
Answer: TCGA UUIDS to TCGA barcode (SampleID) in R
by
aUser
▴ 30
Great solutions on this page, the old web page has been replace with new one, so you need to use the new link, and it will work: old lin…
Comment: Issues With Cram -> Fastq from GTEx v8 WGS
by
Pierre Lindenbaum
160k
unless your cram in sorted on query rather than on coordinate, your cram must be first sort processed with collate: https://twitter.com/lh…
Answer: error in wigToBigWig while converting mappability to bedgraph
by
Pierre Lindenbaum
160k
remove the spaces from your "chrom" key variableStep chrom=NT_173277 span=5 or may be quote the chrom variableStep chrom="NT_173277.1 C…
Comment: DEG (Differential expression gene) analysis
by
dsull
★ 5.6k
Well, I guess expression could be measured from the DNA indirectly such as with RNA Pol II binding to DNA via ChIP-seq but then the OP shou…
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