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1,000 results • Page 7 of 20
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22
votes
11
replies
3.4k
views
Forum: ExpressionSet in the age of tidyverse
expressionset R bioconductor
updated 11 months ago by 43k • written 6.0 years ago by 13k
22
votes
20
replies
4.9k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam bqsr
updated 11 months ago by 43k • written 5.6 years ago by ▴ 150
22
votes
14
replies
25k
views
11 follow
searching reads with a certain sequence in fastq file
grep fastq
updated 10 months ago by • 0 • written 9.1 years ago by ▴ 140
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 26 days ago by 43k • written 4.6 years ago by ★ 1.4k
22
votes
21
replies
4.8k
views
7 follow
Quick Programming Challenge: Calculate Common And Unique Regions From A List Of Chromosome Segments
programming
updated 6 months ago by 43k • written 14.1 years ago by 18k
22
votes
8
replies
6.6k
views
Tool: BioTuring Browser: Making single-cell sequencing data in published studies really accessible!
scRNA-Seq single-cell
updated 10 months ago by 43k • written 5.6 years ago by ▴ 580
22
votes
12
replies
1.8k
views
6 follow
Forum: What were the most impactful Bioinformatics papers published this year
papers publications
updated 11 months ago by 43k • written 4.4 years ago by ▴ 520
22
votes
10
replies
8.8k
views
9 follow
fastq compression tools of choice
fastq compression
updated 12 weeks ago by • 0 • written 8.7 years ago by ▴ 590
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA ComBat R Batch-effect
updated 5 weeks ago by 43k • written 7.9 years ago by ▴ 280
22
votes
8
replies
8.7k
views
7 follow
Gene Expression: Clustering Co-Expressed Genes
gene clustering microarray
updated 6 months ago by 43k • written 14.1 years ago by 11k
22
votes
7
replies
25k
views
What Does The "N50" Mean?
assembly
updated 6 months ago by 43k • written 14.1 years ago by ★ 1.1k
22
votes
16
replies
12k
views
6 follow
List All The Tools Or Write A Script To Validate That A Sequence Only Contains Letters From A Given Alphabet
dna sequence
updated 6 months ago by 43k • written 14.2 years ago by ★ 1.0k
22
votes
17
replies
4.0k
views
Tool: epic: new ChIP-Seq caller based on the SICER algorithm
ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 960
21
votes
12
replies
3.6k
views
Forum: How to Use Biostars Part-3: Formatting Text and Using GitHub Gists
meta how-to documentation
3 months ago by Ram 43k
21
votes
7
replies
12k
views
Forum: Bioinformatics short paper journal resource [software/webapps/database]
journal software webapp
updated 7 months ago by ▴ 100 • written 8.1 years ago by 11k
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit Surv survival curves R
updated 7 weeks ago by • 0 • written 4.6 years ago by ▴ 130
21
votes
18
replies
1.8k
views
Forum: Is it safe to keep our data in github
github
updated 11 months ago by 43k • written 4.0 years ago by ▴ 70
21
votes
20
replies
9.5k
views
11 follow
Laptops for bioinformatics
hardware Laptops
updated 10 months ago by 4.2k • written 18 months ago by ▴ 40
21
votes
7
replies
16k
views
6 follow
GFA to Fasta file
sequence
updated 4 months ago by ▴ 40 • written 8.4 years ago by ▴ 90
21
votes
9
replies
23k
views
9 follow
Building Snpeff Database
vcftools snp gatk
updated 8 months ago by 43k • written 11.8 years ago by ▴ 830
21
votes
15
replies
8.9k
views
10 follow
To What Degree Could We Determine Whether A Gene Is Expressed?
fpkm rna-seq
updated 10 months ago by ★ 1.2k • written 10.2 years ago by ▴ 210
21
votes
12
replies
8.8k
views
10 follow
How To Find A 28Bp 'Primer' Sequence In A Genome?
sequence genome primer
updated 6 months ago by 43k • written 14.2 years ago by ▴ 530
21
votes
26
replies
9.7k
views
11 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 8 weeks ago by ▴ 30 • written 4.4 years ago by 8.6k
21
votes
13
replies
11k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 6 months ago by • 0 • written 22 months ago by 82k
21
votes
13
replies
3.3k
views
11 follow
Biology Database Project
programming dataset
updated 11 months ago by • 0 • written 12.3 years ago by ▴ 10
21
votes
9
replies
13k
views
8 follow
List all available databases for ANNOVAR
annovar
updated 8 months ago by • 0 • written 7.9 years ago by ★ 2.5k
21
votes
11
replies
2.6k
views
6 follow
Forum: Rust bioinformatics projects ideas
projects scRNA-seq RNA-seq Rust
updated 5 months ago by 22k • written 14 months ago by ▴ 150
21
votes
11
replies
11k
views
Tool: Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping next-gen
updated 10 months ago by 43k • written 11.6 years ago by 11k
21
votes
10
replies
35k
views
6 follow
read depth using samtools
depth samtools
updated 8 months ago by ▴ 10 • written 5.4 years ago by ▴ 30
21
votes
11
replies
2.0k
views
Forum: Most important International Big Data Projects: Genetics and Epigenetics
big-data
updated 11 months ago by 43k • written 5.8 years ago by ★ 9.4k
21
votes
14
replies
9.5k
views
Tool: trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization igv ChIP-Seq R bigwigs
updated 11 months ago by 43k • written 3.5 years ago by ★ 3.2k
21
votes
15
replies
2.1k
views
9 follow
Forum: Working abroad without a PhD
career
updated 11 months ago by 43k • written 4.6 years ago by ★ 1.4k
21
votes
11
replies
17k
views
the problem with rpkm (and tpm)
RNA-Seq next-gen gene-expression normalization
updated 10 months ago by ▴ 280 • written 9.6 years ago by ▴ 180
21
votes
13
replies
10k
views
8 follow
Blast Motif With Regular Expression ?
blast motif
updated 6 months ago by 43k • written 14.1 years ago by ▴ 80
21
votes
8
replies
37k
views
8 follow
Merging/Concatenating Vcf Files
vcftools snp indel
updated 8 months ago by ▴ 330 • written 11.7 years ago by ▴ 830
20
votes
10
replies
12k
views
Looking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
taxonomy blast pipeline ncbi
updated 10 months ago by 43k • written 12.3 years ago by ★ 4.0k
20
votes
10
replies
3.5k
views
Agile Programming For Bioinformaticians - Any Suggestions?
general
updated 7 months ago by 43k • written 14.2 years ago by 28k
20
votes
7
replies
3.2k
views
k-mer counting into R using perfect hashing
k-mer Rcpp Cpp hashing R
updated 11 months ago by 43k • written 7.9 years ago by ▴ 120
20
votes
10
replies
17k
views
Could you please explain Fold change, % of change, and log2 fold change (L2FC) to a layment?
gene RNA-Seq next-gen fold-change
updated 8 months ago by 43k • written 4.5 years ago by ▴ 760
20
votes
5
replies
5.6k
views
Check Ancestry Relation Between Go Terms
gene
updated 10 months ago by 43k • written 13.1 years ago by ▴ 990
20
votes
24
replies
6.9k
views
6 follow
Forum: Python or R
RNA-Seq alignment next-gen-sequencing
updated 11 months ago by 43k • written 6.0 years ago by ▴ 160
20
votes
10
replies
9.3k
views
6 follow
Programatic Technique For Gene-Name/Id Conversion
python conversion
updated 6 months ago by 43k • written 14.2 years ago by 4.5k
20
votes
11
replies
2.7k
views
7 follow
samtools sort operation very slow, bottle-neck is external hard drive?
samtools BAM
updated 10 months ago by 43k • written 16 months ago by ▴ 20
20
votes
17
replies
3.3k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by ★ 1.2k • written 3.3 years ago by ▴ 110
20
votes
9
replies
3.1k
views
I Was Studying A Gene But It Disappeared In The Latest Ensembl Release. What Should I Do Now?
ensembl gene-annotation
updated 6 months ago by 43k • written 14.2 years ago by 28k
20
votes
26
replies
3.2k
views
Is there a command line tool that can take an alignment fasta and input and outputs an image?
alignment fasta image
updated 9 months ago by 21k • written 4.9 years ago by ▴ 210
20
votes
10
replies
14k
views
8 follow
Test Whether The Variance In A Group Is Lower Than In Another
statistics r
updated 6 months ago by 43k • written 14.1 years ago by 28k
20
votes
5
replies
3.4k
views
How Do I Import Data From A Torrent Into A Bioperl, R, Bioclipse, Or Taverna Application?
R bioperl torrent
updated 6 months ago by 43k • written 14.2 years ago by 5.4k
20
votes
6
replies
4.9k
views
Some clarification on enrichment analyses and pathway analyses?
pathview R gene-enrichment RNA-Seq
updated 12 months ago by 43k • written 6.5 years ago by ★ 1.6k
20
votes
16
replies
20k
views
6 follow
Conversion of Gene Name to Ensembl ID
gene RNA-Seq R genome
updated 6 months ago by ▴ 10 • written 4.1 years ago by ▴ 20
1,000 results • Page 7 of 20
Recent Votes
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Answer: Genome Visualization Tools
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
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Recent Replies
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
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file by Trivas ★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R by jared.andrews07 ★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran by GenoMax 142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content by noodle ▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file? by wyuan37 • 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file? by wyuan37 • 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses by LauferVA 4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
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