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128 results • Page 3 of 3
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547
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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
0
votes
0
replies
490
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
484
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
6
votes
1
reply
477
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
2
votes
1
reply
463
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 months ago by 43k • written 4 months ago by ▴ 120
2
votes
0
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436
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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401
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 5 months ago by 43k • written 5 months ago by ★ 3.9k
0
votes
0
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390
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
368
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
1
reply
367
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
367
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
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0
replies
353
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
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347
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 4 months ago by ▴ 120
0
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0
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342
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
1
reply
310
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
304
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
303
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
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300
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
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0
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285
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 4 months ago by ▴ 120
0
votes
0
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279
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
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275
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
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266
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
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263
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
251
views
Tutorial: Parsing HMMER output
HMMER
updated 7 weeks ago by 142k • written 7 weeks ago by ▴ 140
3
votes
0
replies
249
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
11 weeks ago by Novogene ▴ 420
2
votes
0
replies
229
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
11 weeks ago by Novogene ▴ 420
1
vote
0
replies
218
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
26 days ago by Novogene ▴ 420
7
votes
1
reply
181
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 7 days ago by 14k • written 7 days ago by ▴ 360
128 results • Page 3 of 3
Recent Votes
Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
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Recent Replies
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data? by Arton • 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax? by mbrav005 • 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon by sansan_96 ▴ 90
..........
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R by jen ▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Juke34 8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax? by Mensur Dlakic ★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools by dlera.lozano ▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat by Mensur Dlakic ★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr by Ram 43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Ram 43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Prawesh • 0
thanks, it's working now.
Answer: Genome Visualization Tools by GenoMax 142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
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