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114 results • Page
2 of 3
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3
votes
1
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658
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Tutorial:
Coordinate Systems and genomic variant description
coordinate-system
HGVS
normalization
VCF
updated 9 months ago by
Ram
43k • written 9 months ago by
Juke34
8.6k
2
votes
1
reply
474
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq
space
clustering
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
6
votes
1
reply
485
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
1
reply
1.9k
views
Tutorial:
Nonparametric Regression STATA 15
STATA-15
Nonparametric-Regression
STATA
updated 12 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
287
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq
SCSA
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
2
votes
0
replies
731
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 11 months ago by
Ram
43k • written 11 months ago by
Coremine Medical
▴ 20
2
votes
0
replies
593
views
Tutorial:
Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf
sparql
data-management
graph
updated 8 months ago by
Ram
43k • written 8 months ago by
Pierre Lindenbaum
161k
0
votes
0
replies
1.4k
views
Tutorial:
Data Panel In R Commander
R
updated 12 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
1
vote
0
replies
649
views
Tutorial:
common mistakes in using spreadsheets
excel
spreadsheet
structured-data
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
497
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
6 months ago by
rohitsatyam102
▴ 860
2
votes
0
replies
1.2k
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
updated 6 months ago by
Ali
• 0 • written 15 months ago by
firestar
★ 1.6k
4
votes
0
replies
791
views
Tutorial:
How to do GSEA in R for RNAseq data
gsea
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
2
votes
0
replies
3.2k
views
Tutorial:
How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix
Seurat
single-cell
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
621
views
Tutorial:
How to make a perfect heatmap using RNAseq data
heatmap
RNAseq
rstats
11 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
0
replies
2.2k
views
Tutorial:
Deep Learning for Cancer Immunotherapy
keras
tensorflow
updated 12 months ago by
Ram
43k • written 6.3 years ago by
Jeremy Leipzig
22k
1
vote
0
replies
356
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
5 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
700
views
Tutorial:
How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix
scRNA-seq
single-cell
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
0
replies
252
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
11 weeks ago by
Novogene
▴ 420
7
votes
0
replies
613
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
9 months ago by
barslmn
★ 2.1k
0
votes
0
replies
273
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
4 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
696
views
Tutorial:
How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
352
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
1
vote
0
replies
220
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
29 days ago by
Novogene
▴ 420
0
votes
0
replies
305
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
293
views
Tutorial:
Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python
RNA-seq
batch-correction
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
2
votes
0
replies
233
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
11 weeks ago by
Novogene
▴ 420
0
votes
0
replies
8.1k
views
Tutorial:
Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R
eviews
updated 12 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
1.3k
views
Tutorial:
In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence
cloud
dna
sequencing
updated 11 months ago by
Ram
43k • written 5.8 years ago by
corlinp
• 0
0
votes
0
replies
667
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling
R
Computational-Biology
10 months ago by
sinha.shriprakash
▴ 20
1
vote
0
replies
553
views
Tutorial:
How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq
heatmap
rstats
TCGA
6 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
2.6k
views
Tutorial:
GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo
R
data-mining
differential-gene-expression
RNA-Seq
updated 11 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
0
votes
0
replies
695
views
Tutorial:
T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq
TCR
single-cell
computational
biology
8 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
394
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
5 months ago by
rohitsatyam102
▴ 860
1
vote
0
replies
1.5k
views
Tutorial:
Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by
Ram
43k • written 6.4 years ago by
bdolin
▴ 90
1
vote
0
replies
559
views
Tutorial:
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome
rstats
spatial
single-cell
9 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
703
views
Tutorial:
How to convert gene ids in R
computational-biology
gene-id
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
409
views
Tutorial:
download metadata using GEOquery
computational-biology
GEO
metadata
updated 5 months ago by
Ram
43k • written 5 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
257
views
Tutorial:
Parsing HMMER output
HMMER
updated 7 weeks ago by
GenoMax
142k • written 7 weeks ago by
I0110
▴ 140
1
vote
0
replies
293
views
Tutorial:
Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
2
votes
0
replies
1.4k
views
Tutorial:
Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq
next-gen
updated 11 months ago by
Ram
43k • written 5.9 years ago by
elia.brodsky
▴ 340
1
vote
0
replies
371
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
0
replies
347
views
Tutorial:
How to convert sra files to fastq files using parallelized fastq-dump
fastq
sra
3 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
373
views
Tutorial:
4 CITE-seq tutorials
CTIE-seq
4 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
268
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq
SCSA
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
1
vote
0
replies
837
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 6 months ago by
Ram
43k • written 14 months ago by
Milad
▴ 10
3
votes
0
replies
758
views
Tutorial:
best practices for single-cell RNAseq analysis
cell
single
scRNAseq
11 months ago by
Ming Tommy Tang
★ 3.9k
5
votes
0
replies
1.7k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 11 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
0
votes
0
replies
3.6k
views
Tutorial:
SFA (Stochastic Frontier Analysis) STATA 14
R
updated 12 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
6
votes
0
replies
583
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by
zx8754
11k • written 3 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
2.2k
views
Tutorial:
Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 12 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
114 results • Page
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Recent Votes
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
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