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141 results • Page 3 of 3
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Tutorial: How to ask computational biology questions
computational-biology
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
1
vote
0
replies
528
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
640
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
1
vote
2
replies
1.6k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 10 months ago by 43k • written 19 months ago by ▴ 20
1
vote
5
replies
633
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
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 10 months ago by 43k • written 16 months ago by ▴ 420
1
vote
0
replies
257
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
826
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 6 months ago by 43k • written 13 months ago by ▴ 10
1
vote
0
replies
614
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
291
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
3 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
661
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
0
votes
1
reply
1.9k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
1
reply
3.2k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 11 months ago by 43k • written 6.5 years ago by • 0
0
votes
0
replies
678
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
0
votes
0
replies
1.4k
views
Tutorial: Data Panel In R Commander
R
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
8.1k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
0
replies
253
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
1
reply
554
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
267
views
Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
284
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
473
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 850
0
votes
0
replies
3.1k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
2.9k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
2.2k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
1
reply
300
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
229
views
Tutorial: Parsing HMMER output
HMMER
updated 6 weeks ago by 142k • written 6 weeks ago by ▴ 140
0
votes
0
replies
327
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
0
votes
0
replies
264
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
3.6k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
0
votes
0
replies
250
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
3 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
327
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
4
replies
746
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
5 months ago by Coremine Medical ▴ 20
0
votes
0
replies
376
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 4 months ago by 43k • written 4 months ago by ★ 3.9k
0
votes
1
reply
543
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 7 months ago by 82k • written 7 months ago by ▴ 30
0
votes
0
replies
3.7k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
0
replies
377
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 850
0
votes
0
replies
685
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
683
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
11 months ago by Coremine Medical ▴ 20
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 43k • written 5.8 years ago by • 0
141 results • Page 3 of 3
Recent Votes
Answer: ERROR When Using Ensembl Plants Biomart Wget API
Answer: Should I remove these cells? (scRNA 10x 5')
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
A: Fold change - a final explanation
Answer: sc/snRNASeq using cell ranger parameters
mitochondria in single nuclear RNAseq
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Recent Replies
Answer: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t by swbarnes2 14k
Any chance the numerical columns were imported as factors?
Comment: ERROR When Using Ensembl Plants Biomart Wget API by Dora ▴ 10
Thank you very much, that works perfectly :) ! Maybe someone needs to use a plant dataset as an example (instead of human dataset ) in the …
Comment: Truncated Bam Error by guanghao • 0
I also have this problem, but it doesn't work even I remove the Xms32g. The result bam is still malformed.
Answer: DMRcate ranges liftover hg19 to hg38 by aaron.stevens • 0
Hey, I believe they are mapped to hg19 and this is potentially a bigger problem than people realise, I nearly made this mistake and I would…
Comment: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by brandon • 0
This worked beautifully using 'requests.get()' in python, thank you so much!
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by Pierre Lindenbaum 161k
first get the main ID in stringdb: $ wget -qO - "https://string-db.org/api/tsv-no-header/get_string_ids?identifiers=RPS4Y1&species=960…
Comment: Help with DGEList function by marco.barr ▴ 90
Are you sure you've loaded the library properly? Have you checked if edgeR is ticked in the list of installed packages? Double-check it. If…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t by mropri ▴ 150
Hi, I just wanted to update that IEGscore and PCNAscore were linearly dependent (or linear combinations of each other). I tested this using…
Comment: TaxID mapping file by Lada ▴ 30
if I understood correctly, I might need fle `prot.accession2taxid.gz` file? According to the [documentation][1] in column 2 is Accession.ve…
Answer: install package by Pine ▴ 10
To follow on Mathew's reply, one way might be to try and see if you can download and install the package tarball locally: 1. Get the packag…
Comment: agilent human all exon sureselct v7 bed file by MiladAD ▴ 10
God bless you man.
Answer: install package by Mathew ▴ 50
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file by Lada ▴ 30
thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs by Jautis ▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data by drajangirija • 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
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