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119,813 results • Page 2 of 2397
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152
votes
42
replies
183k
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22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 2.6 years ago by 44k • written 12.8 years ago by 20k
151
votes
39
replies
26k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 21 months ago by 44k • written 11.9 years ago by 3.0k
150
votes
33
replies
143k
views
27 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 11 weeks ago by 44k • written 12.8 years ago by ★ 2.9k
149
votes
35
replies
64k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 21 months ago by 44k • written 12.0 years ago by ★ 1.6k
149
votes
33
replies
73k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 2.1 years ago by 44k • written 10.6 years ago by ▴ 520
147
votes
34
replies
56k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 21 months ago by 44k • written 11.7 years ago by 6.1k
145
votes
56
replies
9.6k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 22 months ago by 44k • written 11.7 years ago by 102k
144
votes
14
replies
23k
views
15 follow
What Are The Classic Papers In Bioinformatics?
literature papers history
updated 3.7 years ago by 22k • written 14.1 years ago by 18k
144
votes
22
replies
75k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 18 months ago by 88k • written 7.1 years ago by ★ 1.9k
144
votes
62
replies
13k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 22 months ago by 44k • written 13.8 years ago by ★ 2.9k
143
votes
14
replies
171k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 13 months ago by 44k • written 14.7 years ago by 164k
143
votes
33
replies
32k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 5.7 years ago by ▴ 50 • written 14.5 years ago by 13k
142
votes
21
replies
31k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 2.6 years ago by 44k • written 10.0 years ago by ★ 1.6k
140
votes
18
replies
36k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq alignment next-gen R assembly
updated 10 months ago by 44k • written 5.2 years ago by ▴ 810
139
votes
25
replies
87k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 2.7 years ago by 44k • written 12.6 years ago by ★ 4.3k
138
votes
21
replies
72k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer gene database oncogene tumor
4.2 years ago by Malachi Griffith 20k
138
votes
42
replies
22k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 20 months ago by 4.5k • written 11.5 years ago by ★ 1.6k
136
votes
18
replies
175k
views
16 follow
Blast - Formatting Output
blast format output
updated 2.0 years ago by ▴ 30 • written 11.0 years ago by ▴ 320
136
votes
26
replies
26k
views
14 follow
Best Way For A Beginner To Get Up To Speed On Unix Quickly?
unix perl genomics
updated 22 months ago by 44k • written 12.9 years ago by ▴ 300
136
votes
29
replies
8.2k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 2.6 years ago by 44k • written 14.0 years ago by 22k
135
votes
27
replies
47k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 2.6 years ago by 44k • written 12.7 years ago by 33k
134
votes
65
replies
7.3k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate
updated 18 months ago by 44k • written 5.0 years ago by ▴ 920
134
votes
123
replies
41k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 21 months ago by ★ 1.2k • written 6.2 years ago by 88k
133
votes
19
replies
188k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 3.6 years ago by • 0 • written 12.5 years ago by ▴ 370
131
votes
44
replies
38k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 21 months ago by 44k • written 8.2 years ago by ★ 1.1k
131
votes
48
replies
17k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 13.3 years ago by ★ 2.6k • written 13.3 years ago by 11k
130
votes
37
replies
14k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 13.3 years ago by ★ 1.3k • written 13.3 years ago by ▴ 820
129
votes
25
replies
89k
views
20 follow
Sequence Length Distribution From A Fastq File
sequence length fastq
updated 5 months ago by • 0 • written 11.6 years ago by ▴ 390
129
votes
38
replies
10k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 18 months ago by 44k • written 5.7 years ago by 102k
129
votes
33
replies
133k
views
31 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 6 months ago by • 0 • written 13.8 years ago by ▴ 540
128
votes
83
replies
16k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
lossless-fastq-compression fastq-compressor
updated 17 months ago by 44k • written 7.7 years ago by ★ 2.8k
127
votes
46
replies
53k
views
21 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 20 months ago by 44k • written 8.8 years ago by ★ 3.2k
126
votes
7
replies
127k
views
Bam And Indexed Bam Files
bam index
13.0 years ago by Sahel ▴ 270
126
votes
56
replies
110k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 14 months ago by ▴ 40 • written 10.5 years ago by ▴ 380
124
votes
29
replies
41k
views
11 follow
PCA in a RNA seq analysis
RNA-Seq pca
updated 6.1 years ago by 28k • written 7.1 years ago by ▴ 330
124
votes
35
replies
46k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 19 months ago by 44k • written 7.5 years ago by ▴ 830
124
votes
29
replies
7.9k
views
18 follow
What License Do You Use When You Release Code And Data?
software general subjective
updated 13 months ago by 44k • written 14.7 years ago by 7.4k
124
votes
13
replies
181k
views
13 follow
How Can I Convert Bam To Sam?
bam next-gen-sequencing sam
updated 15 months ago by 44k • written 14.4 years ago by 5.0k
122
votes
44
replies
12k
views
24 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 13 months ago by 44k • written 12.0 years ago by 102k
122
votes
31
replies
210k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 13 months ago by 44k • written 14.7 years ago by 11k
122
votes
17
replies
79k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 2.7 years ago by 44k • written 13.6 years ago by ▴ 370
121
votes
44
replies
22k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 22 months ago by 44k • written 14.5 years ago by 5.3k
121
votes
8
replies
81k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 2.9 years ago by 44k • written 10.2 years ago by ▴ 540
121
votes
33
replies
40k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 19 months ago by ★ 2.6k • written 11.3 years ago by 11k
120
votes
23
replies
33k
views
14 follow
Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
cram bam io hdf
updated 3.7 years ago by 44k • written 10.4 years ago by ▴ 320
119
votes
25
replies
125k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 7.8 years ago by ▴ 170 • written 14.4 years ago by 5.0k
118
votes
74
replies
48k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 2.1 years ago by 148k • written 14.0 years ago by ★ 3.3k
118
votes
15
replies
106k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 13.9 years ago by • 0 • written 14.1 years ago by ▴ 210
118
votes
26
replies
38k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 21 months ago by ▴ 230 • written 9.6 years ago by ▴ 610
117
votes
18
replies
41k
views
14 follow
What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
education online
updated 7.6 years ago by ▴ 20 • written 13.4 years ago by ★ 1.3k
119,813 results • Page 2 of 2397
Recent Votes
A: allele frequency bcf tools
The Biostar Handbook. A bioinformatics e-book for beginners.
Comment: Which method should I use to merge scRNA-seq data, Cellranger aggr or Seurat?
Answer: Merging VCF files from different populations
ENA-data brokers, I think you need this...
Comment: Error in conversion of ensembl to gene names
Comment: Python methylation position visualisation
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Recent Replies
Comment: Which method should I use to merge scRNA-seq data, Cellranger aggr or Seurat? by Apprentice ▴ 170
Thank you very much!
Comment: Is there anyone who downloaded Azimuth packges? by ATpoint 86k
Or just `BiocManager::install("satijalab/azimuth")` since this will install from GitHub and take care of CRAN and Bioc dependencies. Wouldn…
Comment: Error in conversion of ensembl to gene names by Dave Carlson ★ 2.1k
If you trim off the version information using the instructions in GenoMax's link above, and then filter on the `ensembl_transcript_id`, it …
Comment: Error in conversion of ensembl to gene names by anasjamshed ▴ 140
its mouse sorrry. But I feel ensembl did not fetch it properly
Comment: Error in conversion of ensembl to gene names by anasjamshed ▴ 140
so if they are transcript ids then how can we convert it into gene names?
Answer: Is there anyone who downloaded Azimuth packges? by pariapooyan • 0
Yes, I finally did :-D install.packages("BiocManager") library(BiocManager) # DirichletMultinomial # if (!requir…
Comment: How should the order of microbiome data preprocessing be prioritized? by ssko ▴ 20
I can't thank you enough for your great answers! @hakimbazol
Comment: Error in conversion of ensembl to gene names by GenoMax 148k
From Mike Smith the developer of BiomaRt: https://www.biostars.org/p/302441/#302485
Comment: Error in conversion of ensembl to gene names by GenoMax 148k
> ENSMUSG00000064336 I feel its not mouse annotation? It is mouse: https://www.ensembl.org/Multi/Search/Results?q=ENSMUSG00000064336
Comment: Error in conversion of ensembl to gene names by Dave Carlson ★ 2.1k
Those are transcript IDs, not gene IDs. That may be at least part of the issue. In my experience some of these methods also do not like h…
Comment: Error in conversion of ensembl to gene names by anasjamshed ▴ 140
ENSMUSG00000064336 I feel its not mouse annotation?
Comment: Which data to choose for correlation examination by lyan125 ▴ 10
Just a small note about this method. After performing multiple tasks, I would need to intersect the results (the genes) with 2 additional d…
Comment: Error in conversion of ensembl to gene names by anasjamshed ▴ 140
"ENSMUST00000000001.5" "ENSMUST00000000003.14" "ENSMUST00000000010.9" "ENSMUST00000000028.14" "ENSMUST00000000033.12" "ENSMUST00000000049…
Answer: Error in conversion of ensembl to gene names by Istvan Albert 102k
sounds like something is not matching, but it is not so easy to debug instead, what you should do is fetch all annotations first, save the…
Answer: Error in conversion of ensembl to gene names by yura.grabovska ▴ 690
Are you able to manually match your `test_ids <- head(ensembl_ids, 10)` by taking one and googling it? Worth doing a sanity check that your…
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